Re: [gmx-users] fftw3f errors despite having the right libraries in the right places installation on MAC
Did start from scratch, and things were normal this time. thank you ! On Fri, Dec 28, 2012 at 2:22 PM, maria goranovic mariagorano...@gmail.comwrote: thank you, Mark. I will try to restart from scratch On Fri, Dec 28, 2012 at 1:10 AM, Mark Abraham mark.j.abra...@gmail.comwrote: Standard procedure is to do ./configure make sudo make install or ./configure --prefix=/somewhere/you/can/write/to make make install I suggest you use sudo to get rid of your progress to date and start again. Using sudo anywhere else is a recipe for trouble. Mark On Thu, Dec 27, 2012 at 3:41 PM, maria goranovic mariagorano...@gmail.comwrote: I will try to fix this. Thank you. Now, the problem I have is that the executables all belong to root, and as a user, I am unable to execute them. How to fix this little one? Maria On Thu, Dec 27, 2012 at 3:36 PM, Mark Abraham mark.j.abra...@gmail.com wrote: sudo should not be necessary for looking in those directories. Whoever set them up has not set up the permissions on them properly. Fix the problem, not the symptoms - you do not want to have to configure software as root, or you are trusting every author of that software not to trash your system accidentally. On Thu, Dec 27, 2012 at 3:31 PM, maria goranovic mariagorano...@gmail.comwrote: turned out to be a sudo problem. without sudo, the compiler could not look into the root directories. sorry for spamming :( On Thu, Dec 27, 2012 at 2:25 PM, maria goranovic mariagorano...@gmail.comwrote: Yes, I can see them in printenv does this have anything to do with single or double precision? On Thu, Dec 27, 2012 at 1:38 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Are those variables actully showing up in your environment? On Thu, Dec 27, 2012 at 11:31 AM, maria goranovic mariagorano...@gmail.comwrote: Dear All I am trying to install 4.5.5 on my mac. I have installed fftw3 with --enable-float, and have used the CPPFLAGS and LDFLAGS options in my .bashrc file. GROMACS still complains that configure: error: Cannot find fftw3f library. Why is it not able to find the libraries? Here are the specific details: content of .bashrc: export CPPFLAGS=-I/usr/local/include export LDFLAGS=-L/usr/local/lib % ls /usr/local/lib/*fft* /usr/local/lib/libfftw3f.a /usr/local/lib/libfftw3f.la % ls /usr/local/include/*fft* /usr/local/include/fftw3.f /usr/local/include/fftw3.f03 /usr/local/include/fftw3.h /usr/local/include/fftw3l.f03 /usr/local/include/fftw3q.f03 Any ideas what might be going wrong? Thank you -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman
Re: [gmx-users] fftw3f errors despite having the right libraries in the right places installation on MAC
thank you, Mark. I will try to restart from scratch On Fri, Dec 28, 2012 at 1:10 AM, Mark Abraham mark.j.abra...@gmail.comwrote: Standard procedure is to do ./configure make sudo make install or ./configure --prefix=/somewhere/you/can/write/to make make install I suggest you use sudo to get rid of your progress to date and start again. Using sudo anywhere else is a recipe for trouble. Mark On Thu, Dec 27, 2012 at 3:41 PM, maria goranovic mariagorano...@gmail.comwrote: I will try to fix this. Thank you. Now, the problem I have is that the executables all belong to root, and as a user, I am unable to execute them. How to fix this little one? Maria On Thu, Dec 27, 2012 at 3:36 PM, Mark Abraham mark.j.abra...@gmail.com wrote: sudo should not be necessary for looking in those directories. Whoever set them up has not set up the permissions on them properly. Fix the problem, not the symptoms - you do not want to have to configure software as root, or you are trusting every author of that software not to trash your system accidentally. On Thu, Dec 27, 2012 at 3:31 PM, maria goranovic mariagorano...@gmail.comwrote: turned out to be a sudo problem. without sudo, the compiler could not look into the root directories. sorry for spamming :( On Thu, Dec 27, 2012 at 2:25 PM, maria goranovic mariagorano...@gmail.comwrote: Yes, I can see them in printenv does this have anything to do with single or double precision? On Thu, Dec 27, 2012 at 1:38 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Are those variables actully showing up in your environment? On Thu, Dec 27, 2012 at 11:31 AM, maria goranovic mariagorano...@gmail.comwrote: Dear All I am trying to install 4.5.5 on my mac. I have installed fftw3 with --enable-float, and have used the CPPFLAGS and LDFLAGS options in my .bashrc file. GROMACS still complains that configure: error: Cannot find fftw3f library. Why is it not able to find the libraries? Here are the specific details: content of .bashrc: export CPPFLAGS=-I/usr/local/include export LDFLAGS=-L/usr/local/lib % ls /usr/local/lib/*fft* /usr/local/lib/libfftw3f.a /usr/local/lib/libfftw3f.la % ls /usr/local/include/*fft* /usr/local/include/fftw3.f /usr/local/include/fftw3.f03 /usr/local/include/fftw3.h /usr/local/include/fftw3l.f03 /usr/local/include/fftw3q.f03 Any ideas what might be going wrong? Thank you -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe
Re: [gmx-users] problems installing 4.5.5 on mac
turns out that the command line tools were not installed by default in
xcode. installing them helped
On Tue, Dec 25, 2012 at 1:43 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
Unfortunately, it means what it says. Xcode by default does not install the
command line compilers, so you might need to Google the solution for that.
Mark
On Tue, Dec 25, 2012 at 1:03 PM, maria goranovic
mariagorano...@gmail.comwrote:
Dear All
I have a macbook pro, with mountain lion, with macports and xcode
installed. When I try to configure gromacs via:
./configure
I get the following error:
checking for C compiler default output file name...
configure: error: in `/Users/mariag/Downloads/gromacs-4.5.5':
configure: error: C compiler cannot create executables
A look into config.log show me this:
#define GMX_QMMM_ORCA /**/
| #define BUILD_TIME Tue Dec 25 13:01:52 CET 2012
| #define BUILD_USER hkhan...@nat-52121.adm.c.sdu.dk
| #define BUILD_MACHINE Darwin 12.2.0 x86_64
| /* end confdefs.h. */
| #include stdio.h
| int
| main ()
| {
| FILE *f = fopen (conftest.out, w);
| return ferror (f) || fclose (f) != 0;
|
| ;
| return 0;
| }
configure:4477: error: in `/Users/hkhandel/Downloads/gromacs-4.5.5':
configure:4481: error: C compiler cannot create executables
See `config.log' for more details.
Any ideas?
Thank you
--
Maria G.
Technical University of Denmark
Copenhagen
--
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--
Maria G.
Technical University of Denmark
Copenhagen
--
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Re: [gmx-users] fftw3f errors despite having the right libraries in the right places installation on MAC
Yes, I can see them in printenv does this have anything to do with single or double precision? On Thu, Dec 27, 2012 at 1:38 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Are those variables actually showing up in your environment? On Thu, Dec 27, 2012 at 11:31 AM, maria goranovic mariagorano...@gmail.comwrote: Dear All I am trying to install 4.5.5 on my mac. I have installed fftw3 with --enable-float, and have used the CPPFLAGS and LDFLAGS options in my .bashrc file. GROMACS still complains that configure: error: Cannot find fftw3f library. Why is it not able to find the libraries? Here are the specific details: content of .bashrc: export CPPFLAGS=-I/usr/local/include export LDFLAGS=-L/usr/local/lib % ls /usr/local/lib/*fft* /usr/local/lib/libfftw3f.a /usr/local/lib/libfftw3f.la % ls /usr/local/include/*fft* /usr/local/include/fftw3.f /usr/local/include/fftw3.f03 /usr/local/include/fftw3.h /usr/local/include/fftw3l.f03 /usr/local/include/fftw3q.f03 Any ideas what might be going wrong? Thank you -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] fftw3f errors despite having the right libraries in the right places installation on MAC
turned out to be a sudo problem. without sudo, the compiler could not look into the root directories. sorry for spamming :( On Thu, Dec 27, 2012 at 2:25 PM, maria goranovic mariagorano...@gmail.comwrote: Yes, I can see them in printenv does this have anything to do with single or double precision? On Thu, Dec 27, 2012 at 1:38 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Are those variables actully showing up in your environment? On Thu, Dec 27, 2012 at 11:31 AM, maria goranovic mariagorano...@gmail.comwrote: Dear All I am trying to install 4.5.5 on my mac. I have installed fftw3 with --enable-float, and have used the CPPFLAGS and LDFLAGS options in my .bashrc file. GROMACS still complains that configure: error: Cannot find fftw3f library. Why is it not able to find the libraries? Here are the specific details: content of .bashrc: export CPPFLAGS=-I/usr/local/include export LDFLAGS=-L/usr/local/lib % ls /usr/local/lib/*fft* /usr/local/lib/libfftw3f.a /usr/local/lib/libfftw3f.la % ls /usr/local/include/*fft* /usr/local/include/fftw3.f /usr/local/include/fftw3.f03 /usr/local/include/fftw3.h /usr/local/include/fftw3l.f03 /usr/local/include/fftw3q.f03 Any ideas what might be going wrong? Thank you -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] fftw3f errors despite having the right libraries in the right places installation on MAC
I will try to fix this. Thank you. Now, the problem I have is that the executables all belong to root, and as a user, I am unable to execute them. How to fix this little one? Maria On Thu, Dec 27, 2012 at 3:36 PM, Mark Abraham mark.j.abra...@gmail.comwrote: sudo should not be necessary for looking in those directories. Whoever set them up has not set up the permissions on them properly. Fix the problem, not the symptoms - you do not want to have to configure software as root, or you are trusting every author of that software not to trash your system accidentally. On Thu, Dec 27, 2012 at 3:31 PM, maria goranovic mariagorano...@gmail.comwrote: turned out to be a sudo problem. without sudo, the compiler could not look into the root directories. sorry for spamming :( On Thu, Dec 27, 2012 at 2:25 PM, maria goranovic mariagorano...@gmail.comwrote: Yes, I can see them in printenv does this have anything to do with single or double precision? On Thu, Dec 27, 2012 at 1:38 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Are those variables actully showing up in your environment? On Thu, Dec 27, 2012 at 11:31 AM, maria goranovic mariagorano...@gmail.comwrote: Dear All I am trying to install 4.5.5 on my mac. I have installed fftw3 with --enable-float, and have used the CPPFLAGS and LDFLAGS options in my .bashrc file. GROMACS still complains that configure: error: Cannot find fftw3f library. Why is it not able to find the libraries? Here are the specific details: content of .bashrc: export CPPFLAGS=-I/usr/local/include export LDFLAGS=-L/usr/local/lib % ls /usr/local/lib/*fft* /usr/local/lib/libfftw3f.a /usr/local/lib/libfftw3f.la % ls /usr/local/include/*fft* /usr/local/include/fftw3.f /usr/local/include/fftw3.f03 /usr/local/include/fftw3.h /usr/local/include/fftw3l.f03 /usr/local/include/fftw3q.f03 Any ideas what might be going wrong? Thank you -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] problems installing 4.5.5 on mac
Dear All
I have a macbook pro, with mountain lion, with macports and xcode
installed. When I try to configure gromacs via:
./configure
I get the following error:
checking for C compiler default output file name...
configure: error: in `/Users/mariag/Downloads/gromacs-4.5.5':
configure: error: C compiler cannot create executables
A look into config.log show me this:
#define GMX_QMMM_ORCA /**/
| #define BUILD_TIME Tue Dec 25 13:01:52 CET 2012
| #define BUILD_USER hkhan...@nat-52121.adm.c.sdu.dk
| #define BUILD_MACHINE Darwin 12.2.0 x86_64
| /* end confdefs.h. */
| #include stdio.h
| int
| main ()
| {
| FILE *f = fopen (conftest.out, w);
| return ferror (f) || fclose (f) != 0;
|
| ;
| return 0;
| }
configure:4477: error: in `/Users/hkhandel/Downloads/gromacs-4.5.5':
configure:4481: error: C compiler cannot create executables
See `config.log' for more details.
Any ideas?
Thank you
--
Maria G.
Technical University of Denmark
Copenhagen
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] course grained fluorinated lipids martini mapping
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Hi I am trying to use g_membed to insert a protein into a bilayer. I made some changes to the sample.mdp file downloaded from the authors' homepage. The changes were: - reduced time step to 0.001 ps (instead of 0.002) - changed constraints to hbonds instead of all-bonds. g_membed runs fine, but stops only after one iteration after which the protein is of course shrunk. The command used is: echo 20 16 | g_membed -f membed.tpr -n membed.ndx -xyinit 0.1 -xyend 1.0 -nxy 1000 -maxwarn 10 I am wondering what is going on ? Also, is there a way to parallelize g_membed? -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] bug in editconf for making a box ? combined two residues into one
Hi I am using editconf to set my box to the right size using: editconf -f in.gro -o out.gro -box 30 30 30 gromacs v. 4.5.3 For this example, my system contains a phosphate anion and a water molecule. After editconf runs, it changes the residue name SOL of the water molecule to the residue name PHO for phosphate, because both have the same residue number (1). Is this not a bug, or am I doing something really silly? One can always try to run a simulation of an amino acid in water, and the error below would be replicated? Interestingly, grompp does not complain that the residue PHO has 8 atoms instead of 5 as in the topology file. I do not see this problem if the residue number of the water molecule is 2 instead of 1. Below are the two .gro files, before and after running the above command. GROtesk MACabre and Sinister 8 1PHOO1P1 13.422 2.753 5.900 1PHO P2 13.250 2.818 5.976 1PHOO2P3 13.193 2.967 5.853 1PHOO3P4 13.263 2.864 6.169 1PHOO4P5 13.118 2.672 5.939 1SOL OW1 12.025 1.421 -1.203 1SOLHW12 12.125 1.421 -1.203 1SOLHW23 11.993 1.516 -1.203 20 20 20 GROtesk MACabre and Sinister 8 1PHOO1P1 15.623 15.449 17.622 1PHO P2 15.451 15.514 17.697 1PHOO2P3 15.394 15.663 17.574 1PHOO3P4 15.464 15.560 17.890 1PHOO4P5 15.319 15.368 17.660 1PHO OW6 14.226 14.117 10.518 1PHOHW17 14.326 14.117 10.518 1PHOHW28 14.194 14.212 10.518 30.0 30.0 30.0 -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] bug in editconf for making a box ? combined two residues into one
Thanks for the replies. I guess it is a very small bug. However, here is another: I have a 2-protein complex in water. The first protein residues numbers are from residues 4 to 14, and the other from 5 to 9. In the INPUT .gro file to grompp, I have a continuous numbering of residues from 4 to 19 (4 to 14+5). However, after an energy minimization, gromacs writes out a .gro file which preserves the original numbering (4 to 14 and 5 to 9) instead of a numbering from 4 to 19. Why does it do that? I can see the problem with such a numbering because I can never unambiguously select residue number 6 if I want to make an index file. How does one go about fixing this? I made the original input .gro file by using : editconf -f in.gro -o out.gro -resnr 4 In the topology file, I read in protein_A.itp and protein_B.itp which start from the original pdb residue number (4 and 5 respectively for the two chains) Thank you for helping, Maria On Wed, Aug 3, 2011 at 3:38 PM, Justin A. Lemkul jalem...@vt.edu wrote: maria goranovic wrote: Hi I am using editconf to set my box to the right size using: editconf -f in.gro -o out.gro -box 30 30 30 gromacs v. 4.5.3 For this example, my system contains a phosphate anion and a water molecule. After editconf runs, it changes the residue name SOL of the water molecule to the residue name PHO for phosphate, because both have the same residue number (1). Is this not a bug, or am I doing something really silly? One can always try to run a simulation of an amino acid in water, and the error below would be replicated? I suspect so. You can file a bug report, but it will probably remain a very low priority for now. One normally does not number a coordinate file this way. Each residue should be numbered independently. Interestingly, grompp does not complain that the residue PHO has 8 atoms instead of 5 as in the topology file. AFAIK grompp only pays attention to atom names, which in this case likely match the topology without an issue. -Justin I do not see this problem if the residue number of the water molecule is 2 instead of 1. Below are the two .gro files, before and after running the above command. GROtesk MACabre and Sinister 8 1PHOO1P1 13.422 2.753 5.900 1PHO P2 13.250 2.818 5.976 1PHOO2P3 13.193 2.967 5.853 1PHOO3P4 13.263 2.864 6.169 1PHOO4P5 13.118 2.672 5.939 1SOL OW1 12.025 1.421 -1.203 1SOLHW12 12.125 1.421 -1.203 1SOLHW23 11.993 1.516 -1.203 20 20 20 GROtesk MACabre and Sinister 8 1PHOO1P1 15.623 15.449 17.622 1PHO P2 15.451 15.514 17.697 1PHOO2P3 15.394 15.663 17.574 1PHOO3P4 15.464 15.560 17.890 1PHOO4P5 15.319 15.368 17.660 1PHO OW6 14.226 14.117 10.518 1PHOHW17 14.326 14.117 10.518 1PHOHW28 14.194 14.212 10.518 30.0 30.0 30.0 -- Maria G. Technical University of Denmark Copenhagen -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: g_bundle -na option for calculating angle between helices
anyone ? :) On Fri, Jul 22, 2011 at 1:19 PM, maria goranovic mariagorano...@gmail.comwrote: Hi I am trying to calculate angle between helices using g_bundle and: http://lists.gromacs.org/pipermail/gmx-users/2007-October/030415.html http://lists.gromacs.org/pipermail/gmx-users/2007-October/030415.htmlI am unable to understand how the -na option works. the program reads 2 index groups and divides them into na parts. I will use -na 2 for 2 axes. But what should the index groups be? with -na 1 I would use the CA atoms on the top and bottom of the helix as the 2 index groups. For 2 helices, should the first index group be the CA atoms at the beginning of the 2 helices? Or should the first index group contain top and bottom CA atoms on the same helix, and the second index group should contain the same for the second helix? Thank you for clarifying -- Maria G. Technical University of Denmark Copenhagen -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_bundle -na option for calculating angle between helices
Hi I am trying to calculate angle between helices using g_bundle and: http://lists.gromacs.org/pipermail/gmx-users/2007-October/030415.html http://lists.gromacs.org/pipermail/gmx-users/2007-October/030415.htmlI am unable to understand how the -na option works. the program reads 2 index groups and divides them into na parts. I will use -na 2 for 2 axes. But what should the index groups be? with -na 1 I would use the CA atoms on the top and bottom of the helix as the 2 index groups. For 2 helices, should the first index group be the CA atoms at the beginning of the 2 helices? Or should the first index group contain top and bottom CA atoms on the same helix, and the second index group should contain the same for the second helix? Thank you for clarifying -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] angle between two domains connected at a hinge
There must be several tools to calculate the angle between two domains connected at a hinge. I was wondering if someone has suggestions on any tools, or whether it is possible to do this using a vmd plugin directly for a trajectory? IN my case, I have a reasonable good idea where the hinge is. I was wondering if the angle between the principal axes of the domains would be good enough? For example, if the domains were two discs attached to a common hinge, how can I find the vector from the hinge in the direction of each disc? -- Maria G. Technical University of Denmark Copenhagen -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] residue HISB not found 4.5.3 versus 4.0.7 OPLSAA
Hi I had a simulation run with 4.0.7, using opls-aa for a protein in water. I now use part of the protein coordinates output from the simulation, and use pdb2gmx as: pdb2gmx -f conf.gro -ff oplsaa -ignh pdb2gmx complains that it cannot find HISB. I checked that the topology files in 4.5.3 do not contain HISB, while those in 4.0.7 do. It does not suffice to create another copy of the HISE topology in the .rtp file and call it HISB, because a number of hydrogen atoms also have been renamed? What can be done? I want to use 4.5.3 because I would prefer to retain residue numbering Maria -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] residue HISB not found 4.5.3 versus 4.0.7 OPLSAA
thought of that, but the trajectory also has HISB data .. so I guess I will have to alter it frame by frame ? On Thu, Jun 16, 2011 at 4:32 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 16/06/2011 11:01 PM, maria goranovic wrote: Hi I had a simulation run with 4.0.7, using opls-aa for a protein in water. I now use part of the protein coordinates output from the simulation, and use pdb2gmx as: pdb2gmx -f conf.gro -ff oplsaa -ignh pdb2gmx complains that it cannot find HISB. I checked that the topology files in 4.5.3 do not contain HISB, while those in 4.0.7 do. It does not suffice to create another copy of the HISE topology in the .rtp file and call it HISB, because a number of hydrogen atoms also have been renamed? What can be done? I want to use 4.5.3 because I would prefer to retain residue numbering Rename all the HISB residues in your input coordinate file to whatever OPLS/AA wants. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] trjcat crashes with error 9360 killed when concatenating large number of frames, bug ?
I am using the command: trjcat -f *gro -o temp.xtc -cat to concatenate about 40,000 frames of 14,000 atoms each. The commands works well for 10,000 frames, but crashes for 40,000 frames after reading all the frames. There is sufficient disk space. Is this a bug of some kind? -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjcat crashes with error 9360 killed when concatenating large number of frames, bug ?
thanks for the help .. will try On Wed, Jun 15, 2011 at 3:02 PM, Justin A. Lemkul jalem...@vt.edu wrote: maria goranovic wrote: I am using the command: trjcat -f *gro -o temp.xtc -cat to concatenate about 40,000 frames of 14,000 atoms each. The commands works well for 10,000 frames, but crashes for 40,000 frames after reading all the frames. There is sufficient disk space. Is this a bug of some kind? Not a bug, but rather clunky code - trjcat consumes a huge amount of memory. If your .gro files are large, then that is the likely limitation. Convert the .gro frames to .xtc with trjconv, then concatenate those instead. -Justin -- Maria G. Technical University of Denmark Copenhagen -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] writing trajectory with water molecules within a distance from protein
An update on this. I got the following to work: 1. use a vmd script closest.tcl (available on the vmd pages) to select closest N waters, and write a pdb file for each frame. 2. however, the above pdb files have different residue numbers for the water molecules for each frame because it is not the same N waters each frame. So use editconf to convert the pdbs to gros with the -resnr 1 option 3. concatenate the frames using trjcat ( -cat option) 4. make the correct time spacing using trjconv. (-timestep) The method is kinda tedious, but the final result is a trajectory of the protein with closest N-waters updated every step. Good enough for my analysis. On Tue, May 10, 2011 at 12:38 PM, Thomas Evangelidis teva...@gmail.comwrote: A work around will be available in the future as a plugin for VMD. For your reference read these threads: http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/14140.html http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/13217.html On 10 May 2011 03:12, Roland Schulz rol...@utk.edu wrote: On Mon, May 9, 2011 at 6:28 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 10/05/2011 12:50 AM, maria goranovic wrote: Dear experts I have a protein simulation in a water box. I now want to write a trajectory containing only the protein, and water molecules within 5 Angstroms of the protein, with the water list being updated each time step. How can one do this? Appreciate the help g_select is useful for dynamic selections of this type. g_select -select help can give examples and such. I'd hope it's been designed so that then using trjconv to extract such selections works, but I can't think how, having not ever tried. g_select writes out one index group per time frame. But trjconv can't use a different index group for each frame. Thus it can't be used to write out a trajectory with those atoms for each frame. Part of the problem is that the trajectory format doesn't support different number of atoms for different frames. What is possible is writing a small script around trjconv to produce one gro/trr file per frame with only those atoms. Roland Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral
Just curious, this would also hold true for the OPLA-AA force field. It is all-atom, so no changes seems to be necessary besides making a d-amino acid in the input ? On Mon, Mar 28, 2011 at 2:13 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 28/03/2011 8:45 PM, maria goranovic wrote: That would mean that a new residue type will not be required? I just need the correct input D-coordinates? Try it, before asking about it :-) I said I suspect you do not need to change anything about the topology, but I haven't actually done anything like this ever. Topologies and code shouldn't care about chirality, so you shouldn't need to do anything other than input the configuration you want. Mark On Sat, Mar 26, 2011 at 2:02 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 26/03/2011 2:27 AM, maria goranovic wrote: Yes, that would be the correct way to do this. I was hoping to take a shorter route, and just modifying a couple of dihedrals in the topology files output by pdb2gmx without having to make a new residue. Is that not possible at all ? Unlike (say) AMBER's leap, pdb2gmx doesn't generate coordinates in a general sense. It generates a topology that matches given coordinates, fixing a few details as directed. It will fill valences with hydrogen atoms, generate terminal groups, organize disulfides, and choose protonation states of titratable residues, but it won't change geometries in the way you seem to want. Neither does anything in the .top/.itp files stipulate the chirality of any center (in all-atom models). Various dihedral angles change sign with chirality, but the dihedral functions are all symmetric about the y-axis (i.e. even). So I suspect you do not need to change anything about the topology. Just use a molecule builder to change the chirality of the relevant center in the input file to pdb2gmx. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral
That would mean that a new residue type will not be required? I just need the correct input D-coordinates? On Sat, Mar 26, 2011 at 2:02 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 26/03/2011 2:27 AM, maria goranovic wrote: Yes, that would be the correct way to do this. I was hoping to take a shorter route, and just modifying a couple of dihedrals in the topology files output by pdb2gmx without having to make a new residue. Is that not possible at all ? Unlike (say) AMBER's leap, pdb2gmx doesn't generate coordinates in a general sense. It generates a topology that matches given coordinates, fixing a few details as directed. It will fill valences with hydrogen atoms, generate terminal groups, organize disulfides, and choose protonation states of titratable residues, but it won't change geometries in the way you seem to want. Neither does anything in the .top/.itp files stipulate the chirality of any center (in all-atom models). Various dihedral angles change sign with chirality, but the dihedral functions are all symmetric about the y-axis (i.e. even). So I suspect you do not need to change anything about the topology. Just use a molecule builder to change the chirality of the relevant center in the input file to pdb2gmx. Mark On Fri, Mar 25, 2011 at 12:24 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Maria, The general solution is to copy the entry in the .rtp file, modify the dihedrals involved, and rename the entry to match the name used in the coordinate (pdb) file. You may also need to copy the entries in the .hdb file, as well as the .tdb files if it is a terminal residue. Hope it helps, Tsjerk On Fri, Mar 25, 2011 at 12:12 PM, maria goranovic mariagorano...@gmail.com wrote: Hi Appreciate the quick help I am sorry, this is not an improper, but a proper dihedral that holds the chirality in place. Then the solution suggested by Meli would not work? I do not have a D-ASP. I in fact have an L-ASP which i want to convert to D. So the question is simply how to set the proper chirality to a D-amino acid in CHARMM. Maria On Fri, Mar 25, 2011 at 11:49 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Maria, The CHARMM force field is an all-atom one. That means it does not require improper dihedrals to maintain chirality. If you have a D-ASP in your structure file, you can rename it to ASP and just run pdb2gmx. Mind not to regenerate hydrogens in that case, or make sure to modify the hydrogen position for the D amino acids afterwards, to set the proper chirality. Hope it helps, Tsjerk On Fri, Mar 25, 2011 at 11:09 AM, maria goranovic mariagorano...@gmail.com wrote: Hello List I want to change an ASP to a D-ASP. I think it should be possible by simply changing 2 improper values around the chiral carbon to their opposite sign. Instead of making a brand new residue, I thought I would take the topology of an ASP generated by pdb2gmx, and simply change values manually in the resulting .itp. However, this is not possible because gromacs wants to read the dihedral parameters from the ffbonded.itp file. Is it possible for me to explicitly state the parameters for these two dihedrals in my d-asp.itp file? This will be the fastest solution to the problem because it precludes making a new residue or defining new atoms types and so on. With the CHARMM force field, I am not sure how q0 cq translate to c0 c1 c2 and c3 which we are used to for gromos topologies. The mailing list search function was down, so I could not explore prior messages about this. -- Maria -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman
[gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral
Hello List I want to change an ASP to a D-ASP. I think it should be possible by simply changing 2 improper values around the chiral carbon to their opposite sign. Instead of making a brand new residue, I thought I would take the topology of an ASP generated by pdb2gmx, and simply change values manually in the resulting .itp. However, this is not possible because gromacs wants to read the dihedral parameters from the ffbonded.itp file. Is it possible for me to explicitly state the parameters for these two dihedrals in my d-asp.itp file? This will be the fastest solution to the problem because it precludes making a new residue or defining new atoms types and so on. With the CHARMM force field, I am not sure how q0 cq translate to c0 c1 c2 and c3 which we are used to for gromos topologies. The mailing list search function was down, so I could not explore prior messages about this. -- Maria -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral
Hi Appreciate the quick help I am sorry, this is not an improper, but a proper dihedral that holds the chirality in place. Then the solution suggested by Meli would not work? I do not have a D-ASP. I in fact have an L-ASP which i want to convert to D. So the question is simply how to set the proper chirality to a D-amino acid in CHARMM. Maria On Fri, Mar 25, 2011 at 11:49 AM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Maria, The CHARMM force field is an all-atom one. That means it does not require improper dihedrals to maintain chirality. If you have a D-ASP in your structure file, you can rename it to ASP and just run pdb2gmx. Mind not to regenerate hydrogens in that case, or make sure to modify the hydrogen position for the D amino acids afterwards, to set the proper chirality. Hope it helps, Tsjerk On Fri, Mar 25, 2011 at 11:09 AM, maria goranovic mariagorano...@gmail.com wrote: Hello List I want to change an ASP to a D-ASP. I think it should be possible by simply changing 2 improper values around the chiral carbon to their opposite sign. Instead of making a brand new residue, I thought I would take the topology of an ASP generated by pdb2gmx, and simply change values manually in the resulting .itp. However, this is not possible because gromacs wants to read the dihedral parameters from the ffbonded.itp file. Is it possible for me to explicitly state the parameters for these two dihedrals in my d-asp.itp file? This will be the fastest solution to the problem because it precludes making a new residue or defining new atoms types and so on. With the CHARMM force field, I am not sure how q0 cq translate to c0 c1 c2 and c3 which we are used to for gromos topologies. The mailing list search function was down, so I could not explore prior messages about this. -- Maria -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral
Yes, that would be the correct way to do this. I was hoping to take a shorter route, and just modifying a couple of dihedrals in the topology files output by pdb2gmx without having to make a new residue. Is that not possible at all ? On Fri, Mar 25, 2011 at 12:24 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Maria, The general solution is to copy the entry in the .rtp file, modify the dihedrals involved, and rename the entry to match the name used in the coordinate (pdb) file. You may also need to copy the entries in the .hdb file, as well as the .tdb files if it is a terminal residue. Hope it helps, Tsjerk On Fri, Mar 25, 2011 at 12:12 PM, maria goranovic mariagorano...@gmail.com wrote: Hi Appreciate the quick help I am sorry, this is not an improper, but a proper dihedral that holds the chirality in place. Then the solution suggested by Meli would not work? I do not have a D-ASP. I in fact have an L-ASP which i want to convert to D. So the question is simply how to set the proper chirality to a D-amino acid in CHARMM. Maria On Fri, Mar 25, 2011 at 11:49 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Maria, The CHARMM force field is an all-atom one. That means it does not require improper dihedrals to maintain chirality. If you have a D-ASP in your structure file, you can rename it to ASP and just run pdb2gmx. Mind not to regenerate hydrogens in that case, or make sure to modify the hydrogen position for the D amino acids afterwards, to set the proper chirality. Hope it helps, Tsjerk On Fri, Mar 25, 2011 at 11:09 AM, maria goranovic mariagorano...@gmail.com wrote: Hello List I want to change an ASP to a D-ASP. I think it should be possible by simply changing 2 improper values around the chiral carbon to their opposite sign. Instead of making a brand new residue, I thought I would take the topology of an ASP generated by pdb2gmx, and simply change values manually in the resulting .itp. However, this is not possible because gromacs wants to read the dihedral parameters from the ffbonded.itp file. Is it possible for me to explicitly state the parameters for these two dihedrals in my d-asp.itp file? This will be the fastest solution to the problem because it precludes making a new residue or defining new atoms types and so on. With the CHARMM force field, I am not sure how q0 cq translate to c0 c1 c2 and c3 which we are used to for gromos topologies. The mailing list search function was down, so I could not explore prior messages about this. -- Maria -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users
Re: [gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx
Just an update, I decided to create a new residue for an isolated GMP. Well, not really, because I used pdb2gmx to output a topology of a dimer, and then modified it carefully to extract the topology of a phosphorylated GTP. thank you ! On Tue, Mar 22, 2011 at 2:52 PM, maria goranovic mariagorano...@gmail.comwrote: the gro file was the input. I am attaching a pdb as well CRYST1100.0100.0100.0 90.00 90.00 90.00 P 1 1 ATOM 1 P G A 4 5.488 -0.842 0.708 1.00 0.00 P ATOM 2 OP1 G A 4 6.418 0.258 1.047 1.00 0.00 O ATOM 3 OP2 G A 4 5.367 -1.998 1.624 1.00 0.00 O ATOM 4 O5' G A 4 4.010 -0.213 0.513 1.00 0.00 O ATOM 5 C5' G A 4 3.816 1.098 0.014 1.00 0.00 C ATOM 6 C4' G A 4 2.324 1.432 -0.121 1.00 0.00 C ATOM 7 O4' G A 4 1.623 0.448 -0.862 1.00 0.00 O ATOM 8 C3' G A 4 1.584 1.482 1.211 1.00 0.00 C ATOM 9 O3' G A 4 1.869 2.669 1.934 1.00 0.00 O ATOM 10 C2' G A 4 0.136 1.413 0.721 1.00 0.00 C ATOM 11 O2' G A 4 -0.363 2.696 0.397 1.00 0.00 O ATOM 12 C1' G A 4 0.241 0.597 -0.574 1.00 0.00 C ATOM 13 N9 G A 4 -0.450 -0.705 -0.438 1.00 0.00 N ATOM 14 C8 G A 4 0.075 -1.954 -0.237 1.00 0.00 C ATOM 15 N7 G A 4 -0.808 -2.911 -0.197 1.00 0.00 N ATOM 16 C5 G A 4 -2.017 -2.251 -0.377 1.00 0.00 C ATOM 17 C6 G A 4 -3.346 -2.767 -0.450 1.00 0.00 C ATOM 18 O6 G A 4 -3.705 -3.941 -0.398 1.00 0.00 O ATOM 19 N1 G A 4 -4.299 -1.762 -0.593 1.00 0.00 N ATOM 20 C2 G A 4 -4.002 -0.413 -0.682 1.00 0.00 C ATOM 21 N2 G A 4 -5.023 0.438 -0.804 1.00 0.00 N ATOM 22 N3 G A 4 -2.751 0.071 -0.652 1.00 0.00 N ATOM 23 C4 G A 4 -1.809 -0.897 -0.499 1.00 0.00 C ATOM 24 H5' G A 4 4.293 1.204 -0.960 1.00 0.00 H ATOM 25 H5'' G A 4 4.269 1.819 0.696 1.00 0.00 H ATOM 26 H4' G A 4 2.217 2.395 -0.623 1.00 0.00 H ATOM 27 H3' G A 4 1.819 0.589 1.792 1.00 0.00 H ATOM 28 H2' G A 4 -0.503 0.940 1.465 1.00 0.00 H ATOM 29 HO2' G A 4 -1.301 2.614 0.210 1.00 0.00 H ATOM 30 H1' G A 4 -0.225 1.145 -1.393 1.00 0.00 H ATOM 31 H8 G A 4 1.129 -2.132 -0.139 1.00 0.00 H ATOM 32 H1 G A 4 -5.265 -2.065 -0.635 1.00 0.00 H ATOM 33 H21 G A 4 -5.974 0.099 -0.815 1.00 0.00 H ATOM 34 H22 G A 4 -4.841 1.428 -0.876 1.00 0.00 H END On Tue, Mar 22, 2011 at 2:43 PM, Daniel Adriano Silva M dadri...@gmail.com wrote: Hi, Is this your input? (a GRO file?). Can you paste the PDB corresponding to the RNA nucleotide that you are interested on? I think the file may be small enough to paste it here so someone can try to reproduce what is happening to you. Daniel 2011/3/22 maria goranovic mariagorano...@gmail.com Sorry for the incomplete reply. version 4.5.3, command: pdb2gmx -f guan.pdb -ignh I tried using -ter, but that did not help. input coordinate file, pulled out from an RNA molecule. Gromacs Runs On Most of All Computer Systems 34 1GP1 5.549 4.916 5.071 1G OP12 5.642 5.026 5.105 1G OP23 5.537 4.800 5.162 1G O5'4 5.401 4.979 5.051 1G C5'5 5.382 5.110 5.001 1G C4'6 5.232 5.143 4.988 1G O4'7 5.162 5.045 4.914 1G C3'8 5.158 5.148 5.121 1G O3'9 5.187 5.267 5.193 1G C2' 10 5.014 5.141 5.072 1G O2' 11 4.964 5.270 5.040 1G C1' 12 5.024 5.060 4.943 1G N9 13 4.955 4.930 4.956 1G C8 14 5.008 4.805 4.976 1G N7 15 4.919 4.709 4.980 1G C5 16 4.798 4.775 4.962 1G C6 17 4.665 4.723 4.955 1G O6 18 4.630 4.606 4.960 1G N1 19 4.570 4.824 4.941 1G C2 20 4.600 4.959 4.932 1G N2 21 4.498 5.044 4.920 1G N3 22 4.725 5.007 4.935 1G C4 23 4.819 4.910 4.950 1G H5' 24 5.429 5.120 4.904 1G H5'' 25 5.427 5.182 5.070 1G H4' 26 5.222 5.240 4.938 1G H3' 27 5.182 5.059 5.179 1G H2' 28 4.950 5.094 5.146 1G HO2' 29 4.870 5.261 5.021 1G H1' 30 4.978 5.115 4.861 1G H8 31 5.113 4.787
Re: [gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx
is this a bug of some kind then? someone ? anyone? just bumping, maria On Mon, Mar 21, 2011 at 10:17 AM, maria goranovic mariagorano...@gmail.comwrote: Here are the contents of my input coordinate file. CRYST10.0000.0000.000 90.00 90.00 90.00 P 1 1 ATOM 1 P G A 4 5.488 -0.842 0.708 1.00 0.00 P ATOM 2 OP1 G A 4 6.418 0.258 1.047 1.00 0.00 O ATOM 3 OP2 G A 4 5.367 -1.998 1.624 1.00 0.00 O ATOM 4 O5' G A 4 4.010 -0.213 0.513 1.00 0.00 O ATOM 5 C5' G A 4 3.816 1.098 0.014 1.00 0.00 C ATOM 6 C4' G A 4 2.324 1.432 -0.121 1.00 0.00 C ATOM 7 O4' G A 4 1.623 0.448 -0.862 1.00 0.00 O ATOM 8 C3' G A 4 1.584 1.482 1.211 1.00 0.00 C ATOM 33 H21 G A 4 -5.974 0.099 -0.815 1.00 0.00 H ATOM 34 H22 G A 4 -4.841 1.428 -0.876 1.00 0.00 H Of course it would be best if pdb2gmx worked as it is if I just have a single nucleotide, and not a chain? Here, I am wondering if the above problem is occurring because pdb2gmx is not being able to deal with an isolated nucleotide (while it might be able to deal with an polymer) Maria On Sat, Mar 19, 2011 at 5:44 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 19/03/11, *maria goranovic * mariagorano...@gmail.com wrote: Dear All I am trying to generate a topology for guanosine monophosphate: i.e. an RNA base with a phosphate at the 5' Carbon. I tried to read in a pdb file containing all atoms, and used pdb2gmx with CHARMM. However, the output coordinate file has no phosphate group on it. Why does the phosphate disappear, and why does pdb2gmx not even give me a warning? That does sound suspicious, but it's hard to say what went wrong. What GROMACS version was it, and what were the contents of your input coordinate file? Assuming that a molecule like GMP does not have a topology, I am guessing I might have to make a new residue within CHARMM. that should not be too much work because there is no new angle/dihedral/bond/atom type to be be added. Can someone please help me with a simple workflow so I do not miss something important? The procedure is outlined here: http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_FieldYour case should be a reasonably straightforward exercise in assigning sensible atom types from the pre-existing options. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx
Sorry for the incomplete reply. version 4.5.3, command: pdb2gmx -f guan.pdb -ignh I tried using -ter, but that did not help. input coordinate file, pulled out from an RNA molecule. Gromacs Runs On Most of All Computer Systems 34 1GP1 5.549 4.916 5.071 1G OP12 5.642 5.026 5.105 1G OP23 5.537 4.800 5.162 1G O5'4 5.401 4.979 5.051 1G C5'5 5.382 5.110 5.001 1G C4'6 5.232 5.143 4.988 1G O4'7 5.162 5.045 4.914 1G C3'8 5.158 5.148 5.121 1G O3'9 5.187 5.267 5.193 1G C2' 10 5.014 5.141 5.072 1G O2' 11 4.964 5.270 5.040 1G C1' 12 5.024 5.060 4.943 1G N9 13 4.955 4.930 4.956 1G C8 14 5.008 4.805 4.976 1G N7 15 4.919 4.709 4.980 1G C5 16 4.798 4.775 4.962 1G C6 17 4.665 4.723 4.955 1G O6 18 4.630 4.606 4.960 1G N1 19 4.570 4.824 4.941 1G C2 20 4.600 4.959 4.932 1G N2 21 4.498 5.044 4.920 1G N3 22 4.725 5.007 4.935 1G C4 23 4.819 4.910 4.950 1G H5' 24 5.429 5.120 4.904 1G H5'' 25 5.427 5.182 5.070 1G H4' 26 5.222 5.240 4.938 1G H3' 27 5.182 5.059 5.179 1G H2' 28 4.950 5.094 5.146 1G HO2' 29 4.870 5.261 5.021 1G H1' 30 4.978 5.115 4.861 1G H8 31 5.113 4.787 4.986 1G H1 32 4.474 4.794 4.936 1G H21 33 4.403 5.010 4.918 1G H22 34 4.516 5.143 4.912 10.0 10.0 10.0 On Tue, Mar 22, 2011 at 2:09 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 22/03/2011 8:15 PM, maria goranovic wrote: is this a bug of some kind then? someone ? anyone? It's still hard to say. I asked you for your GROMACS version and input coordinate file, and you didn't give us either (in full). While you're there, what pdb2gmx command did you use? Mark just bumping, maria On Mon, Mar 21, 2011 at 10:17 AM, maria goranovic mariagorano...@gmail.com wrote: Here are the contents of my input coordinate file. CRYST10.0000.0000.000 90.00 90.00 90.00 P 1 1 ATOM 1 P G A 4 5.488 -0.842 0.708 1.00 0.00 P ATOM 2 OP1 G A 4 6.418 0.258 1.047 1.00 0.00 O ATOM 3 OP2 G A 4 5.367 -1.998 1.624 1.00 0.00 O ATOM 4 O5' G A 4 4.010 -0.213 0.513 1.00 0.00 O ATOM 5 C5' G A 4 3.816 1.098 0.014 1.00 0.00 C ATOM 6 C4' G A 4 2.324 1.432 -0.121 1.00 0.00 C ATOM 7 O4' G A 4 1.623 0.448 -0.862 1.00 0.00 O ATOM 8 C3' G A 4 1.584 1.482 1.211 1.00 0.00 C ATOM 33 H21 G A 4 -5.974 0.099 -0.815 1.00 0.00 H ATOM 34 H22 G A 4 -4.841 1.428 -0.876 1.00 0.00 H Of course it would be best if pdb2gmx worked as it is if I just have a single nucleotide, and not a chain? Here, I am wondering if the above problem is occurring because pdb2gmx is not being able to deal with an isolated nucleotide (while it might be able to deal with an polymer) Maria On Sat, Mar 19, 2011 at 5:44 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 19/03/11, *maria goranovic * mariagorano...@gmail.com wrote: Dear All I am trying to generate a topology for guanosine monophosphate: i.e. an RNA base with a phosphate at the 5' Carbon. I tried to read in a pdb file containing all atoms, and used pdb2gmx with CHARMM. However, the output coordinate file has no phosphate group on it. Why does the phosphate disappear, and why does pdb2gmx not even give me a warning? That does sound suspicious, but it's hard to say what went wrong. What GROMACS version was it, and what were the contents of your input coordinate file? Assuming that a molecule like GMP does not have a topology, I am guessing I might have to make a new residue within CHARMM. that should not be too much work because there is no new angle/dihedral/bond/atom type to be be added. Can someone please help me with a simple workflow so I do not miss something important? The procedure is outlined here: http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_FieldYour case should be a reasonably straightforward exercise in assigning sensible atom types from the pre-existing options. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx
[gmx-users] changing charged groups in CHARMM RNA
Dear List I was looking at the charged groups in a charmm nucleotide, and could see several groups containing 4 to 14 atoms with integer charges. However, the default topology does not have these charged groups. each atom is given a charged group in the default topology. Can we foresee any problems in replacing the default charged groups generated by pdb2gmx by custom-made charged groups of integer values ? Along the same lines, will this lead to a significant increase in performance, besides the advantage of transferability ? Thanking you in advance Maria -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx
the gro file was the input. I am attaching a pdb as well CRYST1100.0100.0100.0 90.00 90.00 90.00 P 1 1 ATOM 1 P G A 4 5.488 -0.842 0.708 1.00 0.00 P ATOM 2 OP1 G A 4 6.418 0.258 1.047 1.00 0.00 O ATOM 3 OP2 G A 4 5.367 -1.998 1.624 1.00 0.00 O ATOM 4 O5' G A 4 4.010 -0.213 0.513 1.00 0.00 O ATOM 5 C5' G A 4 3.816 1.098 0.014 1.00 0.00 C ATOM 6 C4' G A 4 2.324 1.432 -0.121 1.00 0.00 C ATOM 7 O4' G A 4 1.623 0.448 -0.862 1.00 0.00 O ATOM 8 C3' G A 4 1.584 1.482 1.211 1.00 0.00 C ATOM 9 O3' G A 4 1.869 2.669 1.934 1.00 0.00 O ATOM 10 C2' G A 4 0.136 1.413 0.721 1.00 0.00 C ATOM 11 O2' G A 4 -0.363 2.696 0.397 1.00 0.00 O ATOM 12 C1' G A 4 0.241 0.597 -0.574 1.00 0.00 C ATOM 13 N9 G A 4 -0.450 -0.705 -0.438 1.00 0.00 N ATOM 14 C8 G A 4 0.075 -1.954 -0.237 1.00 0.00 C ATOM 15 N7 G A 4 -0.808 -2.911 -0.197 1.00 0.00 N ATOM 16 C5 G A 4 -2.017 -2.251 -0.377 1.00 0.00 C ATOM 17 C6 G A 4 -3.346 -2.767 -0.450 1.00 0.00 C ATOM 18 O6 G A 4 -3.705 -3.941 -0.398 1.00 0.00 O ATOM 19 N1 G A 4 -4.299 -1.762 -0.593 1.00 0.00 N ATOM 20 C2 G A 4 -4.002 -0.413 -0.682 1.00 0.00 C ATOM 21 N2 G A 4 -5.023 0.438 -0.804 1.00 0.00 N ATOM 22 N3 G A 4 -2.751 0.071 -0.652 1.00 0.00 N ATOM 23 C4 G A 4 -1.809 -0.897 -0.499 1.00 0.00 C ATOM 24 H5' G A 4 4.293 1.204 -0.960 1.00 0.00 H ATOM 25 H5'' G A 4 4.269 1.819 0.696 1.00 0.00 H ATOM 26 H4' G A 4 2.217 2.395 -0.623 1.00 0.00 H ATOM 27 H3' G A 4 1.819 0.589 1.792 1.00 0.00 H ATOM 28 H2' G A 4 -0.503 0.940 1.465 1.00 0.00 H ATOM 29 HO2' G A 4 -1.301 2.614 0.210 1.00 0.00 H ATOM 30 H1' G A 4 -0.225 1.145 -1.393 1.00 0.00 H ATOM 31 H8 G A 4 1.129 -2.132 -0.139 1.00 0.00 H ATOM 32 H1 G A 4 -5.265 -2.065 -0.635 1.00 0.00 H ATOM 33 H21 G A 4 -5.974 0.099 -0.815 1.00 0.00 H ATOM 34 H22 G A 4 -4.841 1.428 -0.876 1.00 0.00 H END On Tue, Mar 22, 2011 at 2:43 PM, Daniel Adriano Silva M dadri...@gmail.comwrote: Hi, Is this your input? (a GRO file?). Can you paste the PDB corresponding to the RNA nucleotide that you are interested on? I think the file may be small enough to paste it here so someone can try to reproduce what is happening to you. Daniel 2011/3/22 maria goranovic mariagorano...@gmail.com Sorry for the incomplete reply. version 4.5.3, command: pdb2gmx -f guan.pdb -ignh I tried using -ter, but that did not help. input coordinate file, pulled out from an RNA molecule. Gromacs Runs On Most of All Computer Systems 34 1GP1 5.549 4.916 5.071 1G OP12 5.642 5.026 5.105 1G OP23 5.537 4.800 5.162 1G O5'4 5.401 4.979 5.051 1G C5'5 5.382 5.110 5.001 1G C4'6 5.232 5.143 4.988 1G O4'7 5.162 5.045 4.914 1G C3'8 5.158 5.148 5.121 1G O3'9 5.187 5.267 5.193 1G C2' 10 5.014 5.141 5.072 1G O2' 11 4.964 5.270 5.040 1G C1' 12 5.024 5.060 4.943 1G N9 13 4.955 4.930 4.956 1G C8 14 5.008 4.805 4.976 1G N7 15 4.919 4.709 4.980 1G C5 16 4.798 4.775 4.962 1G C6 17 4.665 4.723 4.955 1G O6 18 4.630 4.606 4.960 1G N1 19 4.570 4.824 4.941 1G C2 20 4.600 4.959 4.932 1G N2 21 4.498 5.044 4.920 1G N3 22 4.725 5.007 4.935 1G C4 23 4.819 4.910 4.950 1G H5' 24 5.429 5.120 4.904 1G H5'' 25 5.427 5.182 5.070 1G H4' 26 5.222 5.240 4.938 1G H3' 27 5.182 5.059 5.179 1G H2' 28 4.950 5.094 5.146 1G HO2' 29 4.870 5.261 5.021 1G H1' 30 4.978 5.115 4.861 1G H8 31 5.113 4.787 4.986 1G H1 32 4.474 4.794 4.936 1G H21 33 4.403 5.010 4.918 1G H22 34 4.516 5.143 4.912 10.0 10.0 10.0 On Tue, Mar 22, 2011 at 2:09 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 22/03/2011 8:15 PM, maria goranovic wrote: is this a bug of some kind then? someone ? anyone? It's still hard to say. I asked you for your GROMACS version and input coordinate file, and you didn't
Re: [gmx-users] changing charged groups in CHARMM RNA
This must be specific to charmm's implementation in gromacs? Out of curiosity, why can one not use charge groups ? On Tue, Mar 22, 2011 at 2:45 PM, Justin A. Lemkul jalem...@vt.edu wrote: maria goranovic wrote: Dear List I was looking at the charged groups in a charmm nucleotide, and could see several groups containing 4 to 14 atoms with integer charges. However, the default topology does not have these charged groups. each atom is given a charged group in the default topology. Can we foresee any problems in replacing the default charged groups generated by pdb2gmx by custom-made charged groups of integer values ? Along the same lines, will this lead to a significant increase in performance, besides the advantage of transferability ? With the CHARMM force field, you should not use charge groups. Each atom should be its own group. -Justin Thanking you in advance Maria -- Maria G. Technical University of Denmark Copenhagen -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] changing charged groups in CHARMM RNA
thank you for the reply. That settles that. On Tue, Mar 22, 2011 at 2:56 PM, Justin A. Lemkul jalem...@vt.edu wrote: maria goranovic wrote: This must be specific to charmm's implementation in gromacs? Out of curiosity, why can one not use charge groups ? http://lists.gromacs.org/pipermail/gmx-users/2010-September/054106.html -Justin On Tue, Mar 22, 2011 at 2:45 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: maria goranovic wrote: Dear List I was looking at the charged groups in a charmm nucleotide, and could see several groups containing 4 to 14 atoms with integer charges. However, the default topology does not have these charged groups. each atom is given a charged group in the default topology. Can we foresee any problems in replacing the default charged groups generated by pdb2gmx by custom-made charged groups of integer values ? Along the same lines, will this lead to a significant increase in performance, besides the advantage of transferability ? With the CHARMM force field, you should not use charge groups. Each atom should be its own group. -Justin Thanking you in advance Maria -- Maria G. Technical University of Denmark Copenhagen -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx
Here are the contents of my input coordinate file. CRYST10.0000.0000.000 90.00 90.00 90.00 P 1 1 ATOM 1 P G A 4 5.488 -0.842 0.708 1.00 0.00 P ATOM 2 OP1 G A 4 6.418 0.258 1.047 1.00 0.00 O ATOM 3 OP2 G A 4 5.367 -1.998 1.624 1.00 0.00 O ATOM 4 O5' G A 4 4.010 -0.213 0.513 1.00 0.00 O ATOM 5 C5' G A 4 3.816 1.098 0.014 1.00 0.00 C ATOM 6 C4' G A 4 2.324 1.432 -0.121 1.00 0.00 C ATOM 7 O4' G A 4 1.623 0.448 -0.862 1.00 0.00 O ATOM 8 C3' G A 4 1.584 1.482 1.211 1.00 0.00 C ATOM 33 H21 G A 4 -5.974 0.099 -0.815 1.00 0.00 H ATOM 34 H22 G A 4 -4.841 1.428 -0.876 1.00 0.00 H Of course it would be best if pdb2gmx worked as it is if I just have a single nucleotide, and not a chain? Here, I am wondering if the above problem is occurring because pdb2gmx is not being able to deal with an isolated nucleotide (while it might be able to deal with an polymer) Maria On Sat, Mar 19, 2011 at 5:44 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 19/03/11, *maria goranovic * mariagorano...@gmail.com wrote: Dear All I am trying to generate a topology for guanosine monophosphate: i.e. an RNA base with a phosphate at the 5' Carbon. I tried to read in a pdb file containing all atoms, and used pdb2gmx with CHARMM. However, the output coordinate file has no phosphate group on it. Why does the phosphate disappear, and why does pdb2gmx not even give me a warning? That does sound suspicious, but it's hard to say what went wrong. What GROMACS version was it, and what were the contents of your input coordinate file? Assuming that a molecule like GMP does not have a topology, I am guessing I might have to make a new residue within CHARMM. that should not be too much work because there is no new angle/dihedral/bond/atom type to be be added. Can someone please help me with a simple workflow so I do not miss something important? The procedure is outlined here: http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_FieldYour case should be a reasonably straightforward exercise in assigning sensible atom types from the pre-existing options. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Nucleosides OPLS-AA
I was also interested in this, and had posted a message about this. I am interested, like the OP, in an isolated nucleotide molecule, such as cytosine or guanidine. Does one have to construct a completely new topology for this? On Fri, Mar 18, 2011 at 9:04 PM, nishap.pa...@utoronto.ca wrote: I know and I apologize, I mistyped. It is an isolated molecule. I did try to combine the parameters of OPLSAA of carbohydrates(Jorgensen, 1997) with the nucleotide base paper (Jorgensen, 1991). However, I am not sure the partial charge that I should use on the Carbon (C) atom of the sugar molecule that is linked with the Nitrogen (N) of nucleoside, because it is not an alcohol anymore. Quoting David van der Spoel sp...@xray.bmc.uu.se: On 2011-03-18 20.41, nishap.pa...@utoronto.ca wrote: I apologize, but I am trying to simulate Cytidine (not cytosine). The parameters are given for cytosine. That's not what you asked for, but in that case you have to combine the cytosine parameters with some kind of sugar ring. Is this in a polymer through the sugar rings as well, or an isolated molecule? Nisha Quoting David van der Spoel sp...@xray.bmc.uu.se: On 2011-03-18 20.14, nishap.pa...@utoronto.ca wrote: Hello, I am trying to use OPLS-AA force field for simulating nucleosides eg. cytosine, adenosine etc. I found parameters for nucleotide bases (eg. 1-methylcytosine) but I haven't been able to find parameters for nucleosides. Does anyone know where I can find parameters for nucleotides for OPLS-AA (if they do exist?). A paper citation would be helpful. Thanks. Nisha Patel It's all there in the atomtypes.atp file, a little fragment: opls_336 12.01100 ; Cytosine C4 Nucleotide base opls_337 12.01100 ; Cytosine C5 parameters: opls_338 12.01100 ; Cytosine C6 JACS,113,2810(1991) opls_339 1.00800 ; Cytosine H-N1 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx
Dear All I am trying to generate a topology for guanosine monophosphate: i.e. an RNA base with a phosphate at the 5' Carbon. I tried to read in a pdb file containing all atoms, and used pdb2gmx with CHARMM. However, the output coordinate file has no phosphate group on it. Why does the phosphate disappear, and why does pdb2gmx not even give me a warning? Assuming that a molecule like GMP does not have a topology, I am guessing I might have to make a new residue within CHARMM. that should not be too much work because there is no new angle/dihedral/bond/atom type to be be added. Can someone please help me with a simple workflow so I do not miss something important? Of course it would be best if pdb2gmx worked as it is if I just have a single nucleotide, and not a chain? -Maria -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] pdb2gmx 4.5.3 fails with free amino acid with amber99sb but runs fine with opls-aa BUG ?
Hello I am trying to pdb2gmx with a free amino acid in amber99sb as follows: pdb2gmx -f temp.pdb -ff amber99sb there are no ter records in the input pdb file. However, pdb2gmx fails with the following error: --- Program pdb2gmx, VERSION 4.5.3 Source code file: pdb2gmx.c, line: 284 Fatal error: In the chosen force field there is no residue type for 'GLU' as a starting terminus For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Is this some kind of bug. If so, is there a workaround? For example, can I have the amino acid bound to the terminus of the larger protein (for which the free amino acid is a ligand) and make the bond have a zero spring constant or something? Maria Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] OPLS force field for RNA nucleotides for protein RNA simulation
Hello I am running a protein-RNA simulation, and was unable to find OLPS-AA topologies for RNA nucleotides. I am aware AMBER or CHARMM are the best force fields for nucleotides, but my protein only simulations were done in OPLS. Can I get any help with OPLS-AA topologies for, say, GMP compatible with gromacs v. 4.5.3. If this is not available, I will try to make these, but where can I find a topology in the first place? Maria Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3
Hi I have a protein whose topology I built using pdb2gmx with the -ss option and the opls-aa force field. When I run grompp, the total charge on the protein is reported as 2.9 (not 2.999). Why a non-zero charge? Does this have something to do with the disulfide bridge? Secondly, when I run a simulation of the same protein (7000 atoms) with certain restraints in vacuum, the simulation runs very slow. I am wondering why. I am not using particle decomposition. the box size is 50 x 50 x 50 nm. Using 4.5.3 -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3
Hi I have figured out the vacuum slow problem. It turns out I was using PBC in vacuum with PME. It is now fixed. The other problem is still there. My protein has 2 chains. one chain is simply a glutamate residue. Its charge (both terminii charged is -1.11 instead of -1). here is the section of the topology with the charges. Why does pdb2gmx assign a charge of -1.11 instead of -1 if there is a free glutamate molecule with NH3+ and COO- at the terminii ? 1 opls_287484GLU N 1 -0.314.0067 ; qtot -0.3 2 opls_290484GLU H1 1 0.33 1.008 ; qtot 0.03 3 opls_290484GLU H2 1 0.33 1.008 ; qtot 0.36 4 opls_290484GLU H3 1 0.33 1.008 ; qtot 0.69 5 opls_283484GLU CA 1 0.04 12.011 ; qtot 0.73 6 opls_140484GLU HA 1 0.06 1.008 ; qtot 0.79 7 opls_136484GLU CB 2 -0.12 12.011 ; qtot 0.67 8 opls_140484GLUHB1 2 0.06 1.008 ; qtot 0.73 9 opls_140484GLUHB2 2 0.06 1.008 ; qtot 0.79 10 opls_274484GLU CG 3 -0.22 12.011 ; qtot 0.57 11 opls_140484GLUHG1 3 0.06 1.008 ; qtot 0.63 12 opls_140484GLUHG2 3 0.06 1.008 ; qtot 0.69 13 opls_271484GLU CD 40.7 12.011 ; qtot 1.39 14 opls_272484GLUOE1 4 -0.815.9994 ; qtot 0.59 15 opls_272484GLUOE2 4 -0.815.9994 ; qtot -0.21 16 opls_271484GLU C 50.7 12.011 ; qtot 0.49 17 opls_272484GLU O1 5 -0.815.9994 ; qtot -0.31 18 opls_272484GLU O2 5 -0.815.9994 ; qtot -1.11 On Thu, Jan 20, 2011 at 11:55 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 01/20/11, *maria goranovic * mariagorano...@gmail.com wrote: Hi I have a protein whose topology I built using pdb2gmx with the -ss option and the opls-aa force field. When I run grompp, the total charge on the protein is reported as 2.9 (not 2.999). Why a non-zero charge? Does this have something to do with the disulfide bridge? Something is materially wrong, like mangled termini. Have a look at the resulting structure. Secondly, when I run a simulation of the same protein (7000 atoms) with certain restraints in vacuum, the simulation runs very slow. I am wondering why. I am not using particle decomposition. the box size is 50 x 50 x 50 nm. Using 4.5.3 Have a look at the end of the .log file for some performance data. How are you assessing very slow? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3
I did use -ter and chose -COO and NH3+. Am i supposed to chose Zwitterion_COO- and Zwitterion_NH3+ ? On Thu, Jan 20, 2011 at 12:55 PM, Justin A. Lemkul jalem...@vt.edu wrote: maria goranovic wrote: Hi I have figured out the vacuum slow problem. It turns out I was using PBC in vacuum with PME. It is now fixed. The other problem is still there. My protein has 2 chains. one chain is simply a glutamate residue. Its charge (both terminii charged is -1.11 instead of -1). here is the section of the topology with the charges. Why does pdb2gmx assign a charge of -1.11 instead of -1 if there is a free glutamate molecule with NH3+ and COO- at the terminii ? You're not choosing the termini correctly. Use -ter with pdb2gmx and select the zwitterion forms of both termini. -Justin 1 opls_287484GLU N 1 -0.314.0067 ; qtot -0.3 2 opls_290484GLU H1 1 0.33 1.008 ; qtot 0.03 3 opls_290484GLU H2 1 0.33 1.008 ; qtot 0.36 4 opls_290484GLU H3 1 0.33 1.008 ; qtot 0.69 5 opls_283484GLU CA 1 0.04 12.011 ; qtot 0.73 6 opls_140484GLU HA 1 0.06 1.008 ; qtot 0.79 7 opls_136484GLU CB 2 -0.12 12.011 ; qtot 0.67 8 opls_140484GLUHB1 2 0.06 1.008 ; qtot 0.73 9 opls_140484GLUHB2 2 0.06 1.008 ; qtot 0.79 10 opls_274484GLU CG 3 -0.22 12.011 ; qtot 0.57 11 opls_140484GLUHG1 3 0.06 1.008 ; qtot 0.63 12 opls_140484GLUHG2 3 0.06 1.008 ; qtot 0.69 13 opls_271484GLU CD 40.7 12.011 ; qtot 1.39 14 opls_272484GLUOE1 4 -0.815.9994 ; qtot 0.59 15 opls_272484GLUOE2 4 -0.815.9994 ; qtot -0.21 16 opls_271484GLU C 50.7 12.011 ; qtot 0.49 17 opls_272484GLU O1 5 -0.815.9994 ; qtot -0.31 18 opls_272484GLU O2 5 -0.815.9994 ; qtot -1.11 On Thu, Jan 20, 2011 at 11:55 AM, Mark Abraham mark.abra...@anu.edu.aumailto: mark.abra...@anu.edu.au wrote: On 01/20/11, *maria goranovic * mariagorano...@gmail.com mailto:mariagorano...@gmail.com wrote: Hi I have a protein whose topology I built using pdb2gmx with the -ss option and the opls-aa force field. When I run grompp, the total charge on the protein is reported as 2.9 (not 2.999). Why a non-zero charge? Does this have something to do with the disulfide bridge? Something is materially wrong, like mangled termini. Have a look at the resulting structure. Secondly, when I run a simulation of the same protein (7000 atoms) with certain restraints in vacuum, the simulation runs very slow. I am wondering why. I am not using particle decomposition. the box size is 50 x 50 x 50 nm. Using 4.5.3 Have a look at the end of the .log file for some performance data. How are you assessing very slow? Mark -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org
Re: [gmx-users] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3
Gee. My mistake then. I did not realize the difference between -COO and Zwitterion_COO-. However, when I use the zwitterion termini on both ends of the other chain, the total charge is 4.010, which is also *slightly*´ disturbing. I have seen numbers like 2.99, which are still better. Is 4.010 acceptable within rounding off errors? thank you for helping -Maria On Thu, Jan 20, 2011 at 2:00 PM, Justin A. Lemkul jalem...@vt.edu wrote: maria goranovic wrote: I did use -ter and chose -COO and NH3+. Am i supposed to chose Zwitterion_COO- and Zwitterion_NH3+ ? That's what I said, and that's what you have, isn't it? A single amino acid that should have both its termini charged? -Justin On Thu, Jan 20, 2011 at 12:55 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: maria goranovic wrote: Hi I have figured out the vacuum slow problem. It turns out I was using PBC in vacuum with PME. It is now fixed. The other problem is still there. My protein has 2 chains. one chain is simply a glutamate residue. Its charge (both terminii charged is -1.11 instead of -1). here is the section of the topology with the charges. Why does pdb2gmx assign a charge of -1.11 instead of -1 if there is a free glutamate molecule with NH3+ and COO- at the terminii ? You're not choosing the termini correctly. Use -ter with pdb2gmx and select the zwitterion forms of both termini. -Justin 1 opls_287484GLU N 1 -0.3 14.0067 ; qtot -0.3 2 opls_290484GLU H1 1 0.33 1.008 ; qtot 0.03 3 opls_290484GLU H2 1 0.33 1.008 ; qtot 0.36 4 opls_290484GLU H3 1 0.33 1.008 ; qtot 0.69 5 opls_283484GLU CA 1 0.04 12.011 ; qtot 0.73 6 opls_140484GLU HA 1 0.06 1.008 ; qtot 0.79 7 opls_136484GLU CB 2 -0.12 12.011 ; qtot 0.67 8 opls_140484GLUHB1 2 0.06 1.008 ; qtot 0.73 9 opls_140484GLUHB2 2 0.06 1.008 ; qtot 0.79 10 opls_274484GLU CG 3 -0.22 12.011 ; qtot 0.57 11 opls_140484GLUHG1 3 0.06 1.008 ; qtot 0.63 12 opls_140484GLUHG2 3 0.06 1.008 ; qtot 0.69 13 opls_271484GLU CD 40.7 12.011 ; qtot 1.39 14 opls_272484GLUOE1 4 -0.8 15.9994 ; qtot 0.59 15 opls_272484GLUOE2 4 -0.8 15.9994 ; qtot -0.21 16 opls_271484GLU C 50.7 12.011 ; qtot 0.49 17 opls_272484GLU O1 5 -0.8 15.9994 ; qtot -0.31 18 opls_272484GLU O2 5 -0.8 15.9994 ; qtot -1.11 On Thu, Jan 20, 2011 at 11:55 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 01/20/11, *maria goranovic * mariagorano...@gmail.com mailto:mariagorano...@gmail.com mailto:mariagorano...@gmail.com mailto:mariagorano...@gmail.com wrote: Hi I have a protein whose topology I built using pdb2gmx with the -ss option and the opls-aa force field. When I run grompp, the total charge on the protein is reported as 2.9 (not 2.999). Why a non-zero charge? Does this have something to do with the disulfide bridge? Something is materially wrong, like mangled termini. Have a look at the resulting structure. Secondly, when I run a simulation of the same protein (7000 atoms) with certain restraints in vacuum, the simulation runs very slow. I am wondering why. I am not using particle decomposition. the box size is 50 x 50 x 50 nm. Using 4.5.3 Have a look at the end of the .log file for some performance data. How are you assessing very slow? Mark -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org
Re: [gmx-users] reading tpx file version 73 with version 58 program
you have generated your em1.tpr file using a newer gromacs version, and are trying to read it with an older gromacs version. Please make sure you use the same gromacs version. Try typing which grompp to find out. On Fri, Dec 24, 2010 at 8:49 AM, shikha agarwal shikhaiiit...@gmail.comwrote: hi , Mr. justin thanx a lot for ur help! now i m able to generate system_inflated.gro. but while i m performing Run energy minimization accorning to tutorial getting this error grompp -f minim.mdp -c pope.gro -p topol_pope.top -o em1.tpr mdrun -v -s em1 -o em1 -c after_em -g emlog Fatal error: reading tpx file (em1.tpr) version 73 with version 58 program with regards: shikha IIIT-A -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] deciphering the output of g_helixorient ?
Dear All I am trying to use g_helixorient to calculate the tilt of a peptide. This one is modeled with MARTINI. I am selecting all backbone atoms of the 23-residue peptide as my index group and am using g_helixorient as follows: g_helixorient -s peptide.tpr -f peptide.xtc -n peptide.ndx -otilt tilt.xvg The output tilt.xvg appears to contain a number for every residue at each time step, with a starting and a trailing zero i.e. a 26-column (time + 0 + 23 values + 0) file. Does one need to take an average over all residues? How does on interpret the output? Merry christmas to all. -Maria -- Maria G. Technical University of Denmark Copenhagen -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Problem with large number of frames only one frame can be read from trajectory bug ?
Resolved: I have found the error. Apparently I was using -dt 20, and the condition that t mod dt = first time (ps) was not being met because the first time was a funny number. Have rectified it. Apologies for the inconvenience. -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Problem with large number of frames only one frame can be read from trajectory bug ?
I have a trajectory containing around 30,000 frames at 20 ps intervals. When I try to read and analyze this trajectory, most gmx tools can read only one frame. I do not know which one. For example, g_density will read the entire trajectory, but will finally report that : read 1 frame from trajectory. calculating ... When I compress the trajectory to one frame every 500 ps, the gmx tools run fine. It seems to be an overflow issue? Is this a bug ? If so, how can it be fixed? - -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] restraining atoms to the plane at the bilayer center: pull code ?
Hmm. I am getting the desired output now, at least as far as the pulled
atoms are concerned, they are all close to the bilayer center (was not so in
a free simulation), and therefore my suspicion is that the code is working.
Just to re-iterate, the atoms to be pulled to the bilayer center were
present at the lipid-water interface in both leaflets.
Here is the (apparently successful) pull code:
; COM PULLING
pull= umbrella
pull_geometry = position
pull_dim= N N Y
pull_start= no
pull_nstxout= 5000
pull_nstfout= 5000
pull_ngroups= 2
pull_group0 = POPC
; global atom number of a POPC atom in the middle of the xy box
pull_pbcatom0 = 3100
pull_group1 = C35TOP
; global atom number of a C35 atom in the middle of the xy box
pull_pbcatom1 = 5467
pull_init1 = 0 0 0.0
pull_rate1 = 0
pull_k1 = 500
pull_vec1 = 0 0 0
pull_group2 = C35BOT
; global atom number of a C35 atom in the middle of the xy box
pull_pbcatom2 = 7755
pull_init2 = 0 0 0.0
pull_rate2 = 0
pull_k2 = 500
pull_vec2 = 0 0 0
##
Here is the output from grompp
Pull group natoms pbc atom distance at start reference at t=0
0 4992 3100
116 5467 0.000 0.000 3.184 0.000 0.000 0.000
216 7755 -0.000 0.000 -3.160 0.000 0.000 0.000
###
The average COM pull En. and potential from the log file after 100 ps.
2.96054e+03
###
And here is the output in the log files, detailing the pulling parameters
pull = umbrella
pull_geometry= position
pull_dim (3):
pull_dim[0]=0
pull_dim[1]=0
pull_dim[2]=1
pull_r1 = 1
pull_r0 = 1.5
pull_constr_tol = 1e-06
pull_nstxout = 5000
pull_nstfout = 5000
pull_ngrp= 2
pull_group 0:
atom (4992):
atom[0,...,4991] = {0,...,4991}
weight: not available
pbcatom = 3099
vec (3):
vec[0]= 0.0e+00
vec[1]= 0.0e+00
vec[2]= 0.0e+00
init (3):
init[0]= 0.0e+00
init[1]= 0.0e+00
init[2]= 0.0e+00
rate = 0
k= 0
kB = 0
pull_group 1:
atom (16):
atom[0]=5026
atom[1]=5114
atom[2]=5202
atom[3]=5290
atom[4]=5378
atom[5]=5466
atom[6]=5554
atom[7]=5642
atom[8]=5730
atom[9]=5818
atom[10]=5906
atom[11]=5994
atom[12]=6082
atom[13]=6169
atom[14]=6258
atom[15]=6346
weight: not available
pbcatom = 5466
vec (3):
vec[0]= 0.0e+00
vec[1]= 0.0e+00
vec[2]= 0.0e+00
init (3):
init[0]= 0.0e+00
init[1]= 0.0e+00
init[2]= 0.0e+00
rate = 0
k= 500
kB = 500
pull_group 2:
atom (16):
atom[0]=6434
atom[1]=6522
atom[2]=6610
atom[3]=6698
atom[4]=6786
atom[5]=6874
atom[6]=6962
atom[7]=7050
atom[8]=7138
atom[9]=7226
atom[10]=7314
atom[11]=7402
atom[12]=7490
atom[13]=7578
atom[14]=7666
atom[15]=7754
weight: not available
pbcatom = 7754
vec (3):
vec[0]= 0.0e+00
vec[1]= 0.0e+00
vec[2]= 0.0e+00
init (3):
init[0]= 0.0e+00
init[1]= 0.0e+00
init[2]= 0.0e+00
rate = 0
k= 500
kB = 500
#
I would want to make sure I am doing this right
Best Wishes
Maria
On Wed, Sep 8, 2010 at 4:09 PM, chris.ne...@utoronto.ca wrote:
Maria,
I highly doubt that you are correct. If you want more help, please copy and
paste your commands and some relevant output back to the list.
Chris.
--original message --
Message: 4
Date: Wed, 8 Sep 2010 15:07:15 +0200
From: maria goranovic mariagorano...@gmail.com
Subject: Re: [gmx-users] restraining atoms to the plane at the bilayer
center:pull code ?
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
aanlkti=rqv+ozsff0u5pmxsuaq-jpjaghnnvpdrjm...@mail.gmail.com
Content-Type: text/plain; charset=iso-8859-1
Dear Chris,
Thank you for the code. I did check out pull_pbcatomN, and thank you for
the
heads up that it is a global index. I used a central atom in the box for
each of the two groups as pull_pbcatom.
After using the code below with a rate constant of ~ 5500 for about 100 ps,
I realized that the atoms in different leaflets were being pulled
Re: [gmx-users] restraining atoms to the plane at the bilayer center: pull code ?
Dear Chris, Thank you for the code. I did check out pull_pbcatomN, and thank you for the heads up that it is a global index. I used a central atom in the box for each of the two groups as pull_pbcatom. After using the code below with a rate constant of ~ 5500 for about 100 ps, I realized that the atoms in different leaflets were being pulled in the same direction. I wanted certain atoms of either leaflet to be restrained to the bilayer center. However, the code pulls all the atoms in the same direction, such that atoms from one leaflet do approach the bilayer center, but those from the other leaflet tend to get further away from the bilayer center. Thus, one actually needs two groups to be pulled, one each for the atoms in each leaflet. Once this was fixed, the code worked just fine. Again, thank you. Maria On Tue, Sep 7, 2010 at 3:40 PM, chris.ne...@utoronto.ca wrote: Maria, try this. There actually is a lot of this on the mailing list, so I suggest checking it a little deeper for your next querry, or at least outlining how you looked and what you found so that it is clear you have tried. Also, read about pull_pbcatomN and think carefully about how you want to set that up. It is a *global* index. ; COM PULLING pull = umbrella pull_geometry= position pull_dim = N N Y pull_start = no pull_nstxout = 500 pull_nstfout = 500 pull_ngroups = 1 pull_group0 = bilayer-group pull_pbcatom0= 0 pull_group1 = pulled-group pull_pbcatom1= 0 pull_init1 = 0 0 0.0 pull_rate1 = 0 pull_k1 = force-constant pull_vec1= 0 0 0 -- original message -- The manual does discuss restraining to a plane, but this must be the plane in which the atom is already present. [ position_restraints ] ; ai functfc ... 3 1 1000 0 0 How about restraining the atom to some other plane? For example, how about restraining a phosphate group initially at the lipid-water interface to the bilayer center (for whatever fancy reasons) ? Won't this require pulling the atom to that plane first? If it can be achieved using the position restraints alone, it is not clear to me how to do this? -Maria On Tue, Sep 7, 2010 at 12:53 PM, Justin A. Lemkul jalemkul at vt.edu wrote: maria goranovic wrote: I want to restrain certain atoms of my simulation to the plane perpendicular to the bilayer normal, and at the bilayer center. Can someone please provide a quick guide on how to do this? I read the pull-code options, but restraining to a plane did not seem possible? You can restrain atoms to a plane using position restraints. See the manual for an example. -Justin -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] restraining atoms to the plane at the bilayer center: pull code ?
The manual does discuss restraining to a plane, but this must be the plane in which the atom is already present. [ position_restraints ] ; ai functfc ... 3 1 1000 0 0 How about restraining the atom to some other plane? For example, how about restraining a phosphate group initially at the lipid-water interface to the bilayer center (for whatever fancy reasons) ? Won't this require pulling the atom to that plane first? If it can be achieved using the position restraints alone, it is not clear to me how to do this? -Maria On Tue, Sep 7, 2010 at 12:53 PM, Justin A. Lemkul jalem...@vt.edu wrote: maria goranovic wrote: I want to restrain certain atoms of my simulation to the plane perpendicular to the bilayer normal, and at the bilayer center. Can someone please provide a quick guide on how to do this? I read the pull-code options, but restraining to a plane did not seem possible? You can restrain atoms to a plane using position restraints. See the manual for an example. -Justin -- Maria G. Technical University of Denmark Copenhagen -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: phase shifts during dihedral fitting
giving this a bump .. any suggestions please ? On Mon, Aug 2, 2010 at 12:39 PM, maria goranovic mariagorano...@gmail.comwrote: Friends Why are the phase shifts while making dihedral parameters always 0 or 180, for example near the unsaturated bond of a lipid ? I am trying to fit a function to a dihedral, and my phase shifts are more like 45 and 30 and 120 degrees and the like. Is there any convenience behind using 0 or 180? How essential is that? -- Maria G. Technical University of Denmark Copenhagen -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] phase shifts during dihedral fitting
Friends Why are the phase shifts while making dihedral parameters always 0 or 180, for example near the unsaturated bond of a lipid ? I am trying to fit a function to a dihedral, and my phase shifts are more like 45 and 30 and 120 degrees and the like. Is there any convenience behind using 0 or 180? How essential is that? -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem while removing extra waters from a simulation box, simulation explodes thereafter
Hi I have run a lipid bilayer simulation, which has too much water in it and too few lipids (small bilayer patch, ~ 80 waters per lipid). I have used genconf to multiply the system in the xy direction to increase system size, and then removed water which is z8 angstroms and z92 angstroms using vmd to decrease my system size and remove unrequired water. After I run editconf on the truncated system getting it to the right box size, the energy minimization keeps exploding on me with lincs errors? I think this is because my (0,0,0) does not coincide with one corner of the simulation box. Or is is something else? In either case, how can this be fixed -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] writing patches to combine two molecules into a dimer and getting the combined topology out
Dear Friends I am looking to make the topology of a lipid bonded to a peptide. Although this can be done by defining a new residue in the .rtp, this method may not be the best if I want to repeat the procedure for different residues on the peptide. Is it possible in gromacs to write a patch (like in CHARMM), where one could combine two molecules using some sort of patch? This is probably implemented for proteins anyway, when amino acids are polymerized. The idea is to have individual topologies and coordinates of the lipid and amino acid, and writing some sort of patch to combine these two, by making new bonds, and elminating some old ones. What would be the best (not necassarily the easiest??) to do this? -Maria -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] for a single amino acid with NH3+ and COO- terminii, pdb2gmx gives a total charge of -1.1 in OPLSAA ?
I tried pdb2gmx with an alanine pdb file, with options 5 (opls force field), 0 (NH3+ n-terminus) and 0 (COO- C-terminus). When I run grompp on the output from pdb2gmx, I get a total charge of -1.1. Any ideas why this happens? The same problem is not there if one looks at a dipeptide. Why the problem for a single amino acid? It looks like when pdb2gmx applies patches for the N-terminus and C-terminus to the ends of a protein, it changes atom types for the peptide backbone. If one uses a single amino acid, the patches are applied to the same residue, and hence the odd -1.1 charge? If this is so, is this not a bug? Thank you for inputs, -maria -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] for a single amino acid with NH3+ and COO- terminii, pdb2gmx gives a total charge of -1.1 in OPLSAA ?
that makes sense, thank you Justin On Tue, Jun 1, 2010 at 4:01 PM, Justin A. Lemkul jalem...@vt.edu wrote: maria goranovic wrote: I tried pdb2gmx with an alanine pdb file, with options 5 (opls force field), 0 (NH3+ n-terminus) and 0 (COO- C-terminus). When I run grompp on the output from pdb2gmx, I get a total charge of -1.1. Any ideas why this happens? The same problem is not there if one looks at a dipeptide. Why the problem for a single amino acid? It looks like when pdb2gmx applies patches for the N-terminus and C-terminus to the ends of a protein, it changes atom types for the peptide backbone. If one uses a single amino acid, the patches are applied to the same residue, and hence the odd -1.1 charge? If this is so, is this not a bug? This is not a bug. You're choosing the wrong termini. With OPLS, there is a zwitterion terminus option that you should be using, since a single amino acid with two charged termini is a zwitterion. -Justin Thank you for inputs, -maria -- Maria G. Technical University of Denmark Copenhagen -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center
So lets say that I delete the first frame from the trajectory in which some atoms might have been outside the box. Everything should be within the box once the simulation starts (from the second frame onwards)? So the procedure should work if the reference structure is the second frame? I have tried that, and it fails as well. On Thu, Nov 5, 2009 at 4:40 PM, XAvier Periole x.peri...@rug.nl wrote: The nojump option will not apply the pbc when an atom is crossing the box boundaries ... in your case your bilayer should definitely be in the center of your box and all the atoms in If not ot course it does not work! On Nov 5, 2009, at 4:33 PM, maria goranovic wrote: my starting structure looks quite all right to me. everything is in the box (except the tails of some lipids) .. wonder whats wrong. thank you verymuch for helping On Thu, Nov 5, 2009 at 4:04 PM, XAvier Periole x.peri...@rug.nl wrote: On Nov 5, 2009, at 4:00 PM, maria goranovic wrote: Hi Xavier, Thanks for the clear instructions. The bilayer is not in one piece in the z direction after the -pbc nojump for some reason. the problem might be from your starting structure, everything should be in the box! Or you may be facing strange/funny/incomprehensible behavior ... after the third step, the water is in the right place, but the bilayer has expanded to periodic boxes in the xy plane. so the center of mass of the lipid molecules is not really being centered in the box ? On Thu, Nov 5, 2009 at 3:34 PM, XAvier Periole x.peri...@rug.nl wrote: you need to do: 1- trjconv -pbc nojump; this keeps your bilayer in one piece on the z direction 2- trjconv -center; using the bilayer to center and the system as output; this will translate your bilayer on the z axis and normally not modify it on the xy plan. 3- trjconv -pbc mol; will put your lipids in one piece in the box; I believe this step cn be coupled to the previous quite safely. On Nov 5, 2009, at 3:23 PM, maria goranovic wrote: One more note about -pbc nojump. I typically use -pbc mol. Using pbc nojump succeeds in keeping the center of the bilayer at 0 0 0, but the atoms have moved way out of the simulation box resulting in a dilute system On Thu, Nov 5, 2009 at 2:31 PM, maria goranovic mariagorano...@gmail.com wrote: Centering on one atom has a problem that the lipid diffuses in the plane of the membrane, and as a result, the entire system starts to center around the lipid resulting in a simulation box which translates a lot in the bilayer plane. The splitting is not a problem, yes. But during the simulation period when the bilayer is not split, it diffuses quite a bit along the bilayer normal (after use of -pbc mol, and centering around the lipid center of mass). a plot of the lipid center of mass shows the bilayer diffusing along z, when its not split. On Thu, Nov 5, 2009 at 2:25 PM, XAvier Periole x.peri...@rug.nlwrote: On Nov 5, 2009, at 2:02 PM, Justin A. Lemkul wrote: maria goranovic wrote: I did use -pbc nojump, but that does not help What about entering on a central lipid tail atom, I suggested some time ago? The bilayer probably just splits across periodic boundaries, so this is not really a problem; just a visualization artefact. The splitting is not a problem and I think that centering using one lipid (tail) won't change the problem if the bilayer is cut half! Or the -pbc mol should be applied ... -Justin The drift is about 1 nm per 10 microseconds . (this is a martini simulation) On Thu, Nov 5, 2009 at 1:02 PM, XAvier Periole x.peri...@rug.nlmailto: x.peri...@rug.nl wrote: On Nov 5, 2009, at 12:09 PM, maria goranovic wrote: Hello All (and especially Berk) This is an update of the problem that I was facing earlier. I used to tau_p of 3.0 ps, and the problem does not go away, the bilayers still drifts in the simulation box. So this is probably a bug then? How much is the drift (nm/ns)? Did you use removal of center of mass of the entire system of bilayer/solvent separately? I still cannot understand how to put the bilayer back into the center of the simulation box. As suggested by Justin, I tried to use just one tail atom of a lipid for centering, but that did not work either. I noticed that my bilayer, which is initially at the center of the simulation box, separates into two leaflets at the box edges from the very first step of the simulation itself, but i am not able to correct that using the -center and -boxcenter zero options. Can someone please make a suggestion and help? You have to do use -pbc nojump first and then center ... Thank you so much -Maria -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx
[gmx-users] martini simulation problem with unsaturated lipid
Hello I get this error while running Martini: A list of missing interactions: G96Angle of 1280 missing 1 Molecule type 'DUPC' the first 10 missing interactions, except for exclusions: G96Angle atoms356 global 135 137 138 Does this mean that some terms are reallly missing? --- Program mdrun_mpi, VERSION 4.0.4 Source code file: domdec_top.c, line: 341 Fatal error: 1 of the 4040 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.2 nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck --- Maria ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center
Hi Berk, Shorter tau_p? I thought you suggested 5.0 or 10.0 ps ? On Wed, Sep 2, 2009 at 5:28 PM, Berk Hess g...@hotmail.com wrote: Hi, I also just recalled that we have a bug report open since two years already about drift of the COM: http://bugzilla.gromacs.org/show_bug.cgi?id=165 But in that case double precision did not change anything, so that does not seem to be a precision issue. Here tau_p was 1 ps, but up till now we did not manage to find the source of this problem. Thus it would be useful to see if a shorter tau_p fixes it in your case. Berk -- Date: Wed, 2 Sep 2009 17:21:46 +0200 Subject: Re: [gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center From: mariagorano...@gmail.com To: gmx-users@gromacs.org I will change the tau_p values, and report back. This might take more than a week though. maria On Wed, Sep 2, 2009 at 5:16 PM, Berk Hess g...@hotmail.com wrote: It might actually affect the center of mass motion removal, because you would be scaling your system with 1 +- 1 bit at every step. This could produce consistent rounding in one direction in single precision, causing the system to move in one direction. This is something we should check in general. Often people are using too small tau_p values, like 0.5 or 1 ps, so I advise them to use 5 or 10 ps. But if larger values cause problems in single precision we should be aware of this. Could you report back if changing tau_p solves the drifting problem? Berk -- Date: Wed, 2 Sep 2009 17:06:50 +0200 Subject: Re: [gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center From: mariagorano...@gmail.com To: gmx-users@gromacs.org Oh dear. That is not good. the missing decimal point in tau_p it is a typo all right. but it seems i have used it in the simulations too. thank you for noticing, Xavier. that forces redoing a lot of simulations. that said, it should still not impact the center of mass removal anyway? -maria On Wed, Sep 2, 2009 at 4:50 PM, XAvier Periole x.peri...@rug.nl wrote: your second value for tau_p is missing the . is this a typo? On Sep 2, 2009, at 4:45 PM, maria goranovic wrote: Here are the mdp parameters: title= POPC cpp = /usr/bin/cpp integrator = md tinit= 0.0 dt = 0.030 nsteps = 300 nstcomm = 1 comm-grps = Lipid W ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 3 nstvout = 3 nstfout = 0 nstlog = 3 nstenergy= 3 ns_type = grid nstlist = 10 pbc = xyz rlist= 1.2 ; Method for doing electrostatics = coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r= 15 vdw_type = Shift ; cut-off lengths= rvdw_switch = 0.9 rvdw = 1.2 DispCorr = No ; Temperature coupling = tcoupl = Berendsen tc-grps = Lipid W tau_t= 0.3 0.3 ref_t= 323 323 ; Pressure coupling = Pcoupl = berendsen Pcoupltype = semiisotropic tau_p = 3.030 compressibility = 3e-53e-5 ref_p = 1.01.0 constraints = none constraint_algorithm = Lincs unconstrained_start = no lincs_order = 4 lincs_warnangle = 30 On Wed, Sep 2, 2009 at 4:33 PM, Berk Hess g...@hotmail.com wrote: Hi, I am 99.99% sure that there is no problem with COM motion removal in Gromacs. Could you post your mdp parameters? Berk From: x.peri...@rug.nl To: gmx-users@gromacs.org Subject: Re: [gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center Date: Wed, 2 Sep 2009 16:04:39 +0200 I am not sure how to fix the trajectory that has drifted ... But if your bilayer drifts even if you use a removal of the COM for the water and bilayer separately that means there is problem in the code! And this should be fixed. XAvier. On Sep 2, 2009, at 3:36 PM, maria goranovic wrote: Dear Experts I had posted this earlier, but the problem was not solved by earlier suggestions. So am posting again. I am simulating a POPC bilayer using MARTINI. The simulation ran fine, but the bilayer drifted towards the edge of the box along the bilayer normal, and eventually some of the atoms crossed the box boundaries. In some cases, entire lipid molecules
[gmx-users] parameters for salicylate
Dear All, Are there any parameters for salicylic acid available which can be used with the berger force field for lipids or with the OPLS-compatible Berger force field for lipids ? thank you for the support maria -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center
Dear Experts I had posted this earlier, but the problem was not solved by earlier suggestions. So am posting again. I am simulating a POPC bilayer using MARTINI. The simulation ran fine, but the bilayer drifted towards the edge of the box along the bilayer normal, and eventually some of the atoms crossed the box boundaries. In some cases, entire lipid molecules crossed the box boundaries. I tried to recenter the trajectory, so that the lipid bilayer would be at the center of the box at all times. But for some reason, this does not seem to work? I have tried simulations using a single comm_group for the entire system, as well as separate ones for the lipid and water, but the same problem appears in either case. Typically, for all-atom bilayers, the following set of commands works to correct the drift: first convert original trajectory to a temp. xtc ### echo 3 0 | trjconv -s *tpr -f original.xtc -o temp.xtc -center -boxcenter zero -pbc mol -n popc.ndx then convert temp.xtc to the final trajecory ### echo 3 0 | trjconv -s k*tpr -f temp.xtc -o final.xtc -center -boxcenter zero -pbc mol -n popc.ndx where groups 3 and 0 are the lipid and the whole system respectively, and final.xtc is my final trajectory. However, this does not work for the MARTINI systems. Looking at the final trajectory in VMD, the bilayer is either at the center of the box, or it is split at the box edges, with each monomer being in different leaflets. If I plot the center of mass motion of the entire system in the original trajectory .. the system seems to drift by ~ 2-3 angstroms in one direction. As a result, water center of mass drifts in the opposite direction (because of PBC). Are there any suggestions to sort this out? One option is to write the entire trajectory to .gro files, recenter all of them (depending upon whether the bilayer is in the center or is split at the box edge), and concatenate the gro files again.but this is tedious, even if scripted. Please let me know if i can provide any additional info ? -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center
I will try centering with one of the lipid tail atoms .. that could solve the problem. This the way I have specified the comm_groups: nstcomm = 1 comm-grps = Lipid W OR nstcom = 1 comm-grps = system -Maria On Wed, Sep 2, 2009 at 4:04 PM, XAvier Periole x.peri...@rug.nl wrote: I am not sure how to fix the trajectory that has drifted ... But if your bilayer drifts even if you use a removal of the COM for the water and bilayer separately that means there is problem in the code! And this should be fixed. XAvier. On Sep 2, 2009, at 3:36 PM, maria goranovic wrote: Dear Experts I had posted this earlier, but the problem was not solved by earlier suggestions. So am posting again. I am simulating a POPC bilayer using MARTINI. The simulation ran fine, but the bilayer drifted towards the edge of the box along the bilayer normal, and eventually some of the atoms crossed the box boundaries. In some cases, entire lipid molecules crossed the box boundaries. I tried to recenter the trajectory, so that the lipid bilayer would be at the center of the box at all times. But for some reason, this does not seem to work? I have tried simulations using a single comm_group for the entire system, as well as separate ones for the lipid and water, but the same problem appears in either case. Typically, for all-atom bilayers, the following set of commands works to correct the drift: first convert original trajectory to a temp. xtc ### echo 3 0 | trjconv -s *tpr -f original.xtc -o temp.xtc -center -boxcenter zero -pbc mol -n popc.ndx then convert temp.xtc to the final trajecory ### echo 3 0 | trjconv -s k*tpr -f temp.xtc -o final.xtc -center -boxcenter zero -pbc mol -n popc.ndx where groups 3 and 0 are the lipid and the whole system respectively, and final.xtc is my final trajectory. However, this does not work for the MARTINI systems. Looking at the final trajectory in VMD, the bilayer is either at the center of the box, or it is split at the box edges, with each monomer being in different leaflets. If I plot the center of mass motion of the entire system in the original trajectory .. the system seems to drift by ~ 2-3 angstroms in one direction. As a result, water center of mass drifts in the opposite direction (because of PBC). Are there any suggestions to sort this out? One option is to write the entire trajectory to .gro files, recenter all of them (depending upon whether the bilayer is in the center or is split at the box edge), and concatenate the gro files again.but this is tedious, even if scripted. Please let me know if i can provide any additional info ? -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center
Here are the mdp parameters:
title= POPC
cpp = /usr/bin/cpp
integrator = md
tinit= 0.0
dt = 0.030
nsteps = 300
nstcomm = 1
comm-grps = Lipid W
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 3
nstvout = 3
nstfout = 0
nstlog = 3
nstenergy= 3
ns_type = grid
nstlist = 10
pbc = xyz
rlist= 1.2
; Method for doing electrostatics =
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r= 15
vdw_type = Shift
; cut-off lengths=
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
; Temperature coupling =
tcoupl = Berendsen
tc-grps = Lipid W
tau_t= 0.3 0.3
ref_t= 323 323
; Pressure coupling =
Pcoupl = berendsen
Pcoupltype = semiisotropic
tau_p = 3.030
compressibility = 3e-53e-5
ref_p = 1.01.0
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
On Wed, Sep 2, 2009 at 4:33 PM, Berk Hess g...@hotmail.com wrote:
Hi,
I am 99.99% sure that there is no problem with COM motion removal in
Gromacs.
Could you post your mdp parameters?
Berk
From: x.peri...@rug.nl
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Martini simulation problem in recentering
trajectory so that the bilayer is at the center
Date: Wed, 2 Sep 2009 16:04:39 +0200
I am not sure how to fix the trajectory that has drifted ...
But if your bilayer drifts even if you use a removal of the COM for
the water and
bilayer separately that means there is problem in the code! And this
should be
fixed.
XAvier.
On Sep 2, 2009, at 3:36 PM, maria goranovic wrote:
Dear Experts
I had posted this earlier, but the problem was not solved by earlier
suggestions. So am posting again.
I am simulating a POPC bilayer using MARTINI. The simulation ran
fine, but the bilayer drifted towards the edge of the box along the
bilayer normal, and eventually some of the atoms crossed the box
boundaries. In some cases, entire lipid molecules crossed the box
boundaries. I tried to recenter the trajectory, so that the lipid
bilayer would be at the center of the box at all times. But for some
reason, this does not seem to work? I have tried simulations using a
single comm_group for the entire system, as well as separate ones
for the lipid and water, but the same problem appears in either case.
Typically, for all-atom bilayers, the following set of commands
works to correct the drift:
first convert original trajectory to a temp. xtc ###
echo 3 0 | trjconv -s *tpr -f original.xtc -o temp.xtc -center -
boxcenter zero -pbc mol -n popc.ndx
then convert temp.xtc to the final trajecory ###
echo 3 0 | trjconv -s k*tpr -f temp.xtc -o final.xtc -center -
boxcenter zero -pbc mol -n popc.ndx
where groups 3 and 0 are the lipid and the whole system
respectively, and final.xtc is my final trajectory.
However, this does not work for the MARTINI systems. Looking at the
final trajectory in VMD, the bilayer is either at the center of the
box, or it is split at the box edges, with each monomer being in
different leaflets.
If I plot the center of mass motion of the entire system in the
original trajectory .. the system seems to drift by ~ 2-3 angstroms
in one direction. As a result, water center of mass drifts in the
opposite direction (because of PBC).
Are there any suggestions to sort this out? One option is to write
the entire trajectory to .gro files, recenter all of them (depending
upon whether the bilayer is in the center or is split at the box
edge), and concatenate the gro files again.but this is tedious, even
if scripted.
Please let me know if i can provide any additional info ?
--
Maria G.
Technical University of Denmark
Copenhagen
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Re: [gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center
Oh dear. That is not good. the missing decimal point in tau_p it is a typo
all right. but it seems i have used it in the simulations too. thank you for
noticing, Xavier.
that forces redoing a lot of simulations.
that said, it should still not impact the center of mass removal anyway?
-maria
On Wed, Sep 2, 2009 at 4:50 PM, XAvier Periole x.peri...@rug.nl wrote:
your second value for tau_p is missing the . is this a typo?
On Sep 2, 2009, at 4:45 PM, maria goranovic wrote:
Here are the mdp parameters:
title= POPC
cpp = /usr/bin/cpp
integrator = md
tinit= 0.0
dt = 0.030
nsteps = 300
nstcomm = 1
comm-grps = Lipid W
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 3
nstvout = 3
nstfout = 0
nstlog = 3
nstenergy= 3
ns_type = grid
nstlist = 10
pbc = xyz
rlist= 1.2
; Method for doing electrostatics =
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r= 15
vdw_type = Shift
; cut-off lengths=
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
; Temperature coupling =
tcoupl = Berendsen
tc-grps = Lipid W
tau_t= 0.3 0.3
ref_t= 323 323
; Pressure coupling =
Pcoupl = berendsen
Pcoupltype = semiisotropic
tau_p = 3.030
compressibility = 3e-53e-5
ref_p = 1.01.0
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
On Wed, Sep 2, 2009 at 4:33 PM, Berk Hess g...@hotmail.com wrote:
Hi,
I am 99.99% sure that there is no problem with COM motion removal in
Gromacs.
Could you post your mdp parameters?
Berk
From: x.peri...@rug.nl
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Martini simulation problem in recentering
trajectory so that the bilayer is at the center
Date: Wed, 2 Sep 2009 16:04:39 +0200
I am not sure how to fix the trajectory that has drifted ...
But if your bilayer drifts even if you use a removal of the COM for
the water and
bilayer separately that means there is problem in the code! And this
should be
fixed.
XAvier.
On Sep 2, 2009, at 3:36 PM, maria goranovic wrote:
Dear Experts
I had posted this earlier, but the problem was not solved by earlier
suggestions. So am posting again.
I am simulating a POPC bilayer using MARTINI. The simulation ran
fine, but the bilayer drifted towards the edge of the box along the
bilayer normal, and eventually some of the atoms crossed the box
boundaries. In some cases, entire lipid molecules crossed the box
boundaries. I tried to recenter the trajectory, so that the lipid
bilayer would be at the center of the box at all times. But for some
reason, this does not seem to work? I have tried simulations using a
single comm_group for the entire system, as well as separate ones
for the lipid and water, but the same problem appears in either case.
Typically, for all-atom bilayers, the following set of commands
works to correct the drift:
first convert original trajectory to a temp. xtc ###
echo 3 0 | trjconv -s *tpr -f original.xtc -o temp.xtc -center -
boxcenter zero -pbc mol -n popc.ndx
then convert temp.xtc to the final trajecory ###
echo 3 0 | trjconv -s k*tpr -f temp.xtc -o final.xtc -center -
boxcenter zero -pbc mol -n popc.ndx
where groups 3 and 0 are the lipid and the whole system
respectively, and final.xtc is my final trajectory.
However, this does not work for the MARTINI systems. Looking at the
final trajectory in VMD, the bilayer is either at the center of the
box, or it is split at the box edges, with each monomer being in
different leaflets.
If I plot the center of mass motion of the entire system in the
original trajectory .. the system seems to drift by ~ 2-3 angstroms
in one direction. As a result, water center of mass drifts in the
opposite direction (because of PBC).
Are there any suggestions to sort this out? One option is to write
the entire trajectory to .gro files, recenter all of them (depending
upon whether the bilayer is in the center or is split at the box
edge), and concatenate the gro files again.but this is tedious, even
if scripted.
Please let me know if i can provide any additional info ?
--
Maria G.
Technical University of Denmark
Re: [gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center
I will change the tau_p values, and report back. This might take more than a
week though.
maria
On Wed, Sep 2, 2009 at 5:16 PM, Berk Hess g...@hotmail.com wrote:
It might actually affect the center of mass motion removal,
because you would be scaling your system with 1 +- 1 bit at every step.
This could produce consistent rounding in one direction in single
precision,
causing the system to move in one direction.
This is something we should check in general.
Often people are using too small tau_p values, like 0.5 or 1 ps,
so I advise them to use 5 or 10 ps.
But if larger values cause problems in single precision we should be aware
of this.
Could you report back if changing tau_p solves the drifting problem?
Berk
--
Date: Wed, 2 Sep 2009 17:06:50 +0200
Subject: Re: [gmx-users] Martini simulation problem in recentering
trajectory so that the bilayer is at the center
From: mariagorano...@gmail.com
To: gmx-users@gromacs.org
Oh dear. That is not good. the missing decimal point in tau_p it is a typo
all right. but it seems i have used it in the simulations too. thank you for
noticing, Xavier.
that forces redoing a lot of simulations.
that said, it should still not impact the center of mass removal anyway?
-maria
On Wed, Sep 2, 2009 at 4:50 PM, XAvier Periole x.peri...@rug.nl wrote:
your second value for tau_p is missing the . is this a typo?
On Sep 2, 2009, at 4:45 PM, maria goranovic wrote:
Here are the mdp parameters:
title= POPC
cpp = /usr/bin/cpp
integrator = md
tinit= 0.0
dt = 0.030
nsteps = 300
nstcomm = 1
comm-grps = Lipid W
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 3
nstvout = 3
nstfout = 0
nstlog = 3
nstenergy= 3
ns_type = grid
nstlist = 10
pbc = xyz
rlist= 1.2
; Method for doing electrostatics =
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r= 15
vdw_type = Shift
; cut-off lengths=
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
; Temperature coupling =
tcoupl = Berendsen
tc-grps = Lipid W
tau_t= 0.3 0.3
ref_t= 323 323
; Pressure coupling =
Pcoupl = berendsen
Pcoupltype = semiisotropic
tau_p = 3.030
compressibility = 3e-53e-5
ref_p = 1.01.0
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
On Wed, Sep 2, 2009 at 4:33 PM, Berk Hess g...@hotmail.com wrote:
Hi,
I am 99.99% sure that there is no problem with COM motion removal in
Gromacs.
Could you post your mdp parameters?
Berk
From: x.peri...@rug.nl
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Martini simulation problem in recentering
trajectory so that the bilayer is at the center
Date: Wed, 2 Sep 2009 16:04:39 +0200
I am not sure how to fix the trajectory that has drifted ...
But if your bilayer drifts even if you use a removal of the COM for
the water and
bilayer separately that means there is problem in the code! And this
should be
fixed.
XAvier.
On Sep 2, 2009, at 3:36 PM, maria goranovic wrote:
Dear Experts
I had posted this earlier, but the problem was not solved by earlier
suggestions. So am posting again.
I am simulating a POPC bilayer using MARTINI. The simulation ran
fine, but the bilayer drifted towards the edge of the box along the
bilayer normal, and eventually some of the atoms crossed the box
boundaries. In some cases, entire lipid molecules crossed the box
boundaries. I tried to recenter the trajectory, so that the lipid
bilayer would be at the center of the box at all times. But for some
reason, this does not seem to work? I have tried simulations using a
single comm_group for the entire system, as well as separate ones
for the lipid and water, but the same problem appears in either case.
Typically, for all-atom bilayers, the following set of commands
works to correct the drift:
first convert original trajectory to a temp. xtc ###
echo 3 0 | trjconv -s *tpr -f original.xtc -o temp.xtc -center -
boxcenter zero -pbc mol -n popc.ndx
then convert temp.xtc to the final trajecory ###
echo 3 0 | trjconv -s k*tpr -f temp.xtc -o final.xtc -center -
boxcenter zero -pbc mol -n popc.ndx
where groups 3 and 0
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Does anyone know if the current MARTINI version have parameters for N-terminal and C-terminal caps other than NH3+ and COO- ? Thank you -Maria -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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[gmx-users] how to center a MARTINI trajectory so that the lipid bilayer remains at the center of the box
Dear All, This has been discussed before for individual frames. But I am having a problem in trying to center a trajectory so that the bilayer remains at the center of the box. I have tried several combinations, but none of the them work. In each case, the centering and/or the fitting is done on the lipid bilayer itself. trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -center -boxcenter zero -pbc mol this one works for one particular .gro file, but not for the whole trajectory. I tried all of the following, but none of them work. What is the solution ? trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -center -boxcenter zero trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -pbc mol -boxcenter zero trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -pbc mol -center trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -pbc mol -fit trans trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -pbc mol -fit trans -center trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -pbc mol -fit trans -center -boxcenter zero trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -fit trans trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -fit progressive -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: how to center a MARTINI trajectory so that the lipid bilayer remains at the center of the box (XAvier Periole)
Well the bilayer drifts down in the z-direction, and eventually the leaflets almost separate, with each leaflet being on opposite ends of the box. if i try pbc nojump, the lipids drift far away from the box in the xy plane On Fri, Jul 3, 2009 at 12:00 PM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: how to center a MARTINI trajectory so that the lipid bilayer remains at the center of the box (XAvier Periole) -- Message: 1 Date: Fri, 3 Jul 2009 11:43:55 +0200 From: XAvier Periole x.peri...@rug.nl Subject: Re: [gmx-users] how to center a MARTINI trajectory so that the lipid bilayer remains at the center of the box To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: eea7daa1-6584-4af0-8321-3fea30a41...@rug.nl Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes What is the problem exactly? The two layers separate over the pbc? did you try a -pbc nojump prior the centering? On Jul 3, 2009, at 11:37 AM, maria goranovic wrote: Dear All, This has been discussed before for individual frames. But I am having a problem in trying to center a trajectory so that the bilayer remains at the center of the box. I have tried several combinations, but none of the them work. In each case, the centering and/or the fitting is done on the lipid bilayer itself. trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx - center -boxcenter zero -pbc mol this one works for one particular .gro file, but not for the whole trajectory. I tried all of the following, but none of them work. What is the solution ? trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx - center -boxcenter zero trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -pbc mol -boxcenter zero trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -pbc mol -center trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx - pbc mol -fit trans trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx - pbc mol -fit trans -center trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx - pbc mol -fit trans -center -boxcenter zero trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -fit trans trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -fit progressive -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 63, Issue 11 * -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Re: how to center a MARTINI trajectory so that the lipid bilayer remains at the center of the box (XAvier Periole) (XAvier Periole)
I did remove the center of mass motion from my system. But did not do it separately for the lipids and solvent. Oh dear ... thats not good ... is it ? Is this just a problem which can be corrected after the simulation, or are the simulations now completely useless ? -MAria On Fri, Jul 3, 2009 at 12:27 PM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: protein covalently bond to ligand (Tsjerk Wassenaar) 2. waters in ion channels (Samik Bhattacharya) 3. Re: waters in ion channels (Itamar Kass) 4. Re: how to center a MARTINI trajectory so that thelipid bilayer remains at the center of the box (XAvier Periole) (maria goranovic) 5. Re: Re: how to center a MARTINI trajectory so that thelipid bilayer remains at the center of the box (XAvier Periole) (XAvier Periole) -- Message: 1 Date: Fri, 3 Jul 2009 12:03:48 +0200 From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] protein covalently bond to ligand To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 8ff898150907030303m6d941470j4317dabe6b893...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi haziz...@razi.tums.ac.ir, I think it's better to only use PRODRG for the pyridoxal phosphate part. Then you can process the rest of the protein as usual, preserving the parameters for lysine backbone and side chain. The PLP part you can renumber and merge with the protein topology, adding bond, angles and dihedrals for the connection. Alternatively you could rewrite the PLP topology as a .rtp entry and add the connection in the file specbond.dat. Hope it helps, Tsjerk On Fri, Jul 3, 2009 at 9:03 AM, hazizianhaziz...@razi.tums.ac.ir wrote: Hi I want to do MD with a protien with prydoxal phosphate(PLP) which attache covalently to one lysine. For this I extract the Toplogy of lysine-PLP from PRODRG server.(DRGGMX.ITP and DRGPOH.PDB).I Changed the name DRGGMX.ITP to DRG.itp. after donig pdb2gmx -f m.pdb -o m1.pdb -water spce with the protein without PLP (m.pdb=protein whitout covalent bond) , I modified the topol.top file followig this: 1- add DRG.itp under the forcefield section on topol.top 2- add DRG 1 under the molecule sectin of topol.top also I modifed m1.pdb: cut the related lysine (LYS 360) in the m1.pdb and paste the modified lysine- PLP (DRG 360)coordination from DRGPH.PDB. then I do editconf -f m1.pdb and genbox -f m1.pdb successfully, but when I want to do grompp the following fatal error appeared: There is no DRG moleculetype. what should I do now? Thanks. -- Tehran University of Medical Sciences www.tums.ac.ir -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 -- Message: 2 Date: Fri, 3 Jul 2009 15:38:42 +0530 (IST) From: Samik Bhattacharya samikb...@yahoo.co.in Subject: [gmx-users] waters in ion channels To: Gromacs gmx-users@gromacs.org Message-ID: 920957.8244...@web95412.mail.in2.yahoo.com Content-Type: text/plain; charset=iso-8859-1 hi i'm simulating a ion channel protein in DPPC membrane. i'm following Justin's tutorial for that. and have completed upto the solvation step. but right after solvation, i found some water molecules in the channel. now i want to delete those molecules. in the tutorial it is advised tyo use the keepbyz script to do that.. but after using that i didn't find any change in the structure. watres are still present in there. may be i am making some mistake in running the program or something like that!!! can anyone suggest any thing to solve the problem...thanking you all in advance. Looking for local information? Find it on Yahoo! Local http
[gmx-users] Re: Re: Re: how to center a MARTINI trajectory so that the lipid bilayer remains at the center of the box
Well .. I will rerun the simulations. setting this would do it, right: comm_grps = POPC Solvent where popc and solvent are the 2 groups ? -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problem in Martini simulation with gromacs version 4.0.4 works fine with gromacs 3.3.1 error G96Angle of 2395 missing
Dear All, I ran a POPC simuIation in gromacs 3.3.1 with the martini force field and it ran fine. But I am getting the following error when I run it in gromacs 4.0.4. It seems there is some problem with the way the topology is built, but I cannot find out what the problem is? A list of missing interactions: G96Angle of 2395 missing 1 Molecule type 'POPC' the first 10 missing interactions, except for exclusions: G96Angle atoms9 10 11 global 1933 1934 1935 --- Program mdrun_mpi, VERSION 4.0.4 Source code file: domdec_top.c, line: 341 Fatal error: 1 of the 5532 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.2 nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pair s and tabulated bonds also see option -ddcheck --- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] where is the normalization direction in radial axial g_densmap plots?
I made a radial-axial density plot using g_densmap. What one gets out is a 3-D number density as a function of radial and axial distance from the defined axis. So which is the third direction, and how is it averaged out? Sorry if this is a very elementary question g_densmap -f protein.xtc -s protein.tpr -n proteinndx -o protein.xpm -b 1 -e 3 -bin 0.01 -amax 2 -rmax 2 -dmax 40 -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Recentering box after simulation of self-assembly of a bilayer
Please help ! I ran a simulation of self-assembly of a DPPC lipid bilayer. At the end of the simulation, I have a bilayer, but it is not at the center of the box. Instead, it has two leaflets on each edge of the box separated by water, with the bilayer normal along the x-axis. How can I realign this trajectory, so that I can get the bilayer at the center of the box? It will also be nice to be able to align the membrane with the z-axis as is the norm. I have trialled and errored with many combinations of trjconv, but none seems to work -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re:Re: Recentering box after simulation of self-assembly of a bilayer (Justin A. Lemkul)
Thank you Justin. The following option worked for me: -center -boxcenter zero -pbc mol with the centering done around the lipid. Sincerly -Maria Message: 3 Date: Thu, 07 May 2009 07:41:50 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Recentering box after simulation of self-assembly of abilayer To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4a02c8fe.4050...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed maria goranovic wrote: Please help ! I ran a simulation of self-assembly of a DPPC lipid bilayer. At the end of the simulation, I have a bilayer, but it is not at the center of the box. Instead, it has two leaflets on each edge of the box separated by water, with the bilayer normal along the x-axis. How can I realign this trajectory, so that I can get the bilayer at the center of the box? It will also be nice to be able to align the membrane with the z-axis as is the norm. I have trialled and errored with many combinations of trjconv, but none seems to work Using trjconv -center should work. If it doesn't, you'll have to provide the command lines that you have tried to get more useful advice. Alignment with the z-axis may be tricky. You could, in theory, dump out all the frames from the trajectory (or at least a subset) as .pdb/.gro files, use editconf to rotate all of them, then use trjconv to convert them to .trr/.xtc frames and concatenate with trjcat. This procedure could easily be scripted for convenience. -Justin -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] rotate trajectory from self-assembly of lipid bilayer
Dear Friends I have run a simple self-assembly simulation of a lipid bilayer. When I look at the trajectory, the bilayer normal is aligned along the y-axis, and the bilayer is not centered to the middle of the box, but towards the edge of the box. So, the bilayer is split into its periodic image. I was wondering what would be a good way to center the bilayer in the middle, and perhaps align it along the y-axis too? I know this can be done for a single .gro file using editconf, but how does one to it for a trajectory. I have tried various combinations of -center (zero, rect, tric) and -fit (trans, rot+trans), but nothing seems to work perfectly. I am using 3.3.1 Thanking you -Maria -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] grompp segmentation fault when trying to position restrain water along bilayer normal
Hello I am trying to restrain water along the bilayer normal. For this; 1. I made a posre_solvent.itp using genpr. It look like this: ; position restraints for Solvent [ position_restraints ] ; i funct fcxfcyfcz 340831 0 0 1000 340841 0 0 1000 340851 0 0 1000 ... (there are ~ 60,000 water molecules) 2. I include this file in my topology file using: #ifdef POSRES_SOLVENT #include posre_solvent.itp #endif 3. And finally, the mdp file looks like: .. define = -DFLEX_SPC -DPOSRES_SOLVENT .. Why do I get a segmentation fault on running grompp? Thank u for helping -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] set up self assembly for mixture of lipids using genbox
Hello I am trying to using genbox to set up a random 2-lipid mixture. Is there a way to do this? First, i put 100 POPC molecules randomly in the sim. box. Now I want to add 28 POPS lipids. How can I do this ? thank you for helping out -Maria -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: set up self assembly for mixture of lipids using genbox
That sounds like a good idea. However, what sort of cheap physical model are you suggesting to get rid of the very ordered initial state ? -Maria maria goranovic wrote: Hello I am trying to using genbox to set up a random 2-lipid mixture. Is there a way to do this? First, i put 100 POPC molecules randomly in the sim. box. Now I want to add 28 POPS lipids. How can I do this ? I'm not aware of a direct method for doing this. Creating interstices for arbitrarily shaped molecules is non-trivial. One approach is to choose your lipid mixture and to concatenate cunningly-sized boxes each with a pure sample of one component of the mixture. Then a long equilibration will see the mixtures randomize. You can probably get away with a long pseudo-equilibration period with a very cheap physical model to make sure you get away from the highly ordered state, then a shorter real equilibration to move into the right ensemble from that intermediate point. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Quantitative output for g_mdmat ... a better way to list residue contacts
Dear Experts, I have a protein simulation from which I want to list residue-residue contacts. g_mdmat and xpm2ps provide a nice picture, but it would be nice to just have a list of contacts. Specifically ... which residues make contacts with which other residues. Is there a way to do this? Thank you -Maria -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] OPLS parameters for phospho-tyrosine
Dear All, Has anyone a topology for phosphorylated tyrosine residue in OPLS that can be shared? Sincerely, -Maria -- -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] OPLS parameters for phosphotyrosine?
Dear All, Has anyone a topology for phosphorylated tyrosine residue in OPLS that can be shared? Sincerely, -Maria -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_density problem segmentation fault glibc detected
Here are the answers to the questions: Did see the trajectory. Looks fine Did start from different initial time frames, and thicker slabs, problem does not go away Yes, the simulation has run for ~ 80 ns. It is equilibrated Which log file ? What I reported was from the log file On Tue, Jun 10, 2008 at 3:30 PM, Peyman Yamin [EMAIL PROTECTED] wrote: Have you seen the trajectory? Did you try to start from different frames? Is your system equilibrated? check log file! Peyman On Tuesday 10 June 2008 13:35, himanshu khandelia wrote: Hi, I am trying to calculate the density in a bilayer simulation: echo 27 | g_density -f lipiddrg.xtc -n all.ndx -s all.tpr -o head.xvg -sl 200 -b 4 The system size is about 6.5 x 6.5 x 9.6 I get the following error, after g_density has read most of the trajectory: *** glibc detected *** g_density: free(): invalid next size (fast): 0x00877e70 *** Can anyone please point out what the problem might be? The same command works for other trajectories for me. Thank you -Himanshu MEMPHYS, SDU, Denmark. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik Universitaet Erlangen-Nuernberg Egerlandstr. 3 91058 Erlangen Phone: +49(0) - 9131 - 85 27671 Mailto: [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with simulation of phosphatidic acid, possibly in my topology?
Dear Mark, Sorry, perhaps I should have clarified more. I did not just make a blind substitution of a choline by a H-atom. First, I did conserve charge. Second, I did introduce reasonable non-bonded and bonded interaction parameters for the new H-atom. The non-bonded interaction parameters were similar to those suggested by the mono-anionic phosphate group on a threonine or serine. I guess you will agree force fields are often set up that entire functional groups from one molecule can be transferred to others. For example, one can use the same head group for both POPC and DPPC, or conversely, one can use different types of hydrocarbon chains for the same head group, from 12 carbons to 20 carbons, as has often been done. The only parameters that might change in getting POPA from POPC are near the H-atom itself, and those are the ones that I had posted earlier, just to see if anyone could notice a mistake. Similar methods have been used in literature earlier, except that a DFT calculation was made for the mono-anionic phosphate group to get new charges. The DFT did reveal that charges on DOPA were similar to DOPC. The main issue I have is that I get a somewhat skewed phosphate group that leads to unfavorable positions for the oxygen atoms on phosphate. I am guessing that this is because of the bonded-interactions of the new H-atom. On Mon, May 5, 2008 at 3:10 PM, Mark Abraham [EMAIL PROTECTED] wrote: himanshu khandelia wrote: Hi, I am trying to run a simulation of a POPC bilayer mixed with some mono-anionic Phosphatidic acid (POPA) , where the choline group is replaced by a hydrogen atom. However, the energy of my simulation box diverges, and I am trying to fix the problem. I also tried running a simulation of PA solvated in water and a single sodium ion, but even that does not work. I will try to provide as much detail as possible, I hope someone can help point out some obvious error which I have not been able to debug over 3 days. In the simulation of a single PA molecule in water, MDRUN keeps complaining that the distance between atoms H1 and O4 is very high ( 4 nm or so). The problem probably lies in my topology, possibly in the bonded interactions? Merely replacing a functional group with a hydrogen doesn't make for a sensible model physics. First, you probably didn't conserve charge, and second the parameters don't necessarily make sense for a particle of mass 1 rather than mass 12 (plus secondary effect of substituent group), and third there's no way to fix both the foregoing and the other issues. You need at least to find a proper model of POPA and to implement it, or if need be, develop one yourself. Search the wiki for Parameterization to get a start on the latter, but it is an expert topic. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] timesteps don't match error
Hi, After using gmxcheck on a merged trajectory, I get the following error throughout the trajectory. What does this mean ? Thank you for the help. . Timesteps at t=21610 don't match (8, 10) Reading frame 50 time 21670.002 Timesteps at t=21700 don't match (10, 2) Timesteps at t=21702 don't match (2, 8) Timesteps at t=21710 don't match (8, 10) Reading frame 60 time 21760.002 Timesteps at t=21800 don't match (10, 2) and so on. -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] timesteps don't match error
I used: trjcat -o out.trr -f *trr On Fri, May 2, 2008 at 11:42 AM, Mark Abraham [EMAIL PROTECTED] wrote: maria goranovic wrote: Hi, After using gmxcheck on a merged trajectory, I get the following error throughout the trajectory. What does this mean ? How did you merge the trajectory? Thank you for the help. . Timesteps at t=21610 don't match (8, 10) Reading frame 50 time 21670.002 Timesteps at t=21700 don't match (10, 2) Timesteps at t=21702 don't match (2, 8) Timesteps at t=21710 don't match (8, 10) Reading frame 60 time 21760.002 Timesteps at t=21800 don't match (10, 2) and so on. -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] timesteps don't match error
I have gmxchecked my individual trr files. They should contain 10 frames each, but the output looks like: # Reading frame 10 time 10002.000 Timesteps at t=1 don't match (10, 2) Last frame 10 time 10002.000 Item#frames Step11 Time11 Lambda 11 Coords 11 Velocities 11 Forces 0 Box 11 gcq#54: I'm a Wishbone and I'm Breaking (Pixies) # I think I have some idea of what the problem might be. I use the following method to continue my simulation trajectories: From the minimized structure, I first run a short 2 ps (1000 step) simulation where I assign initial velocities. I obtain out-1.trr and out-1.edr and out-1.gro. I then want to use tpbconv to continue the simulation, like so: tpbconv -f out-1.trr -s out-1.tpr -e out-1.edr -extend 100 -o out-2.tpr However, out-1.tpr cannot be used to continue the simulation, because new velocities would be assigned, and I might want to change some parameter (like removing restraints) when I continue the simulation. So, I then make a new out-1.tpr file based on a dummy .mdp file, which contains all the new parameters for the continuation run, and which looks like: grompp -f dummy.mdp -c out-1.gro -p temp.top -o out-1.tpr ### integrator = md tinit = 0 init_step = 1000 nsteps = 0 dt = 0.002 etc... ### So, the new tpr file suggests that the simulation should start from 1000x 0.002 = 2 ps. This seems to be the source of the problem somehow, because the error when I use gmxcheck on the merger trajectory is typically like: Timesteps at t=21702 don't match (2, 8) So, there seems to be a 2 ps offset. the above output is also not very clear to me. What does (2,8) mean ? I hope this makes things a little more clearer. So there are no missing frames, but how do I fix the timestamps and so ? Thanks a lot for reading the long email and helping out -maria On Fri, May 2, 2008 at 12:25 PM, Xavier Periole [EMAIL PROTECTED] wrote: On Fri, 2 May 2008 12:01:37 +0200 maria goranovic [EMAIL PROTECTED] wrote: I used: trjcat -o out.trr -f *trr It looks like you have missing frames in your xtc files ... that happens sometimes when the simulation is stopped and restarted from the trr file whereas the buffer of the xtc file is not emptied. Did you gmxcheck the xtc files? On Fri, May 2, 2008 at 11:42 AM, Mark Abraham [EMAIL PROTECTED] wrote: maria goranovic wrote: Hi, After using gmxcheck on a merged trajectory, I get the following error throughout the trajectory. What does this mean ? How did you merge the trajectory? Thank you for the help. . Timesteps at t=21610 don't match (8, 10) Reading frame 50 time 21670.002 Timesteps at t=21700 don't match (10, 2) Timesteps at t=21702 don't match (2, 8) Timesteps at t=21710 don't match (8, 10) Reading frame 60 time 21760.002 Timesteps at t=21800 don't match (10, 2) and so on. -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Maria G. Technical University of Denmark Copenhagen - XAvier Periole - PhD NMR Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole http://md.chem.rug.nl/%7Eperiole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Maria G. Technical University of Denmark Copenhagen
Re: [gmx-users] timesteps don't match error
I see. And how can I fix this ? Using trjconv -timestep ? I just want to be sure ... Thank you On Fri, May 2, 2008 at 1:57 PM, Xavier Periole [EMAIL PROTECTED] wrote: You probably fond the problem. trjcat expects 10 ps intervals between frames. If it is not the case it complains. On Fri, 2 May 2008 13:14:07 +0200 maria goranovic [EMAIL PROTECTED] wrote: I have gmxchecked my individual trr files. They should contain 10 frames each, but the output looks like: # Reading frame 10 time 10002.000 Timesteps at t=1 don't match (10, 2) Last frame 10 time 10002.000 Item#frames Step11 Time11 Lambda 11 Coords 11 Velocities 11 Forces 0 Box 11 gcq#54: I'm a Wishbone and I'm Breaking (Pixies) # I think I have some idea of what the problem might be. I use the following method to continue my simulation trajectories: From the minimized structure, I first run a short 2 ps (1000 step) simulation where I assign initial velocities. I obtain out-1.trr and out-1.edr and out-1.gro. I then want to use tpbconv to continue the simulation, like so: tpbconv -f out-1.trr -s out-1.tpr -e out-1.edr -extend 100 -o out-2.tpr However, out-1.tpr cannot be used to continue the simulation, because new velocities would be assigned, and I might want to change some parameter (like removing restraints) when I continue the simulation. So, I then make a new out-1.tpr file based on a dummy .mdp file, which contains all the new parameters for the continuation run, and which looks like: grompp -f dummy.mdp -c out-1.gro -p temp.top -o out-1.tpr ### integrator = md tinit = 0 init_step = 1000 nsteps = 0 dt = 0.002 etc... ### So, the new tpr file suggests that the simulation should start from 1000x 0.002 = 2 ps. This seems to be the source of the problem somehow, because the error when I use gmxcheck on the merger trajectory is typically like: Timesteps at t=21702 don't match (2, 8) So, there seems to be a 2 ps offset. the above output is also not very clear to me. What does (2,8) mean ? I hope this makes things a little more clearer. So there are no missing frames, but how do I fix the timestamps and so ? Thanks a lot for reading the long email and helping out -maria On Fri, May 2, 2008 at 12:25 PM, Xavier Periole [EMAIL PROTECTED] wrote: On Fri, 2 May 2008 12:01:37 +0200 maria goranovic [EMAIL PROTECTED] wrote: I used: trjcat -o out.trr -f *trr It looks like you have missing frames in your xtc files ... that happens sometimes when the simulation is stopped and restarted from the trr file whereas the buffer of the xtc file is not emptied. Did you gmxcheck the xtc files? On Fri, May 2, 2008 at 11:42 AM, Mark Abraham [EMAIL PROTECTED] wrote: maria goranovic wrote: Hi, After using gmxcheck on a merged trajectory, I get the following error throughout the trajectory. What does this mean ? How did you merge the trajectory? Thank you for the help. . Timesteps at t=21610 don't match (8, 10) Reading frame 50 time 21670.002 Timesteps at t=21700 don't match (10, 2) Timesteps at t=21702 don't match (2, 8) Timesteps at t=21710 don't match (8, 10) Reading frame 60 time 21760.002 Timesteps at t=21800 don't match (10, 2) and so on. -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Maria G. Technical University of Denmark Copenhagen
Re: [gmx-users] timesteps don't match error
Yes, I am quite sure I am not missing frames. Do you mean 8 and 10 ARE the different time intervals it found not matching. Thank you, again ! -MAria On Fri, May 2, 2008 at 5:21 PM, Xavier Periole [EMAIL PROTECTED] wrote: On Fri, 2 May 2008 17:06:08 +0200 maria goranovic [EMAIL PROTECTED] wrote: I see. And how can I fix this ? Using trjconv -timestep ? I just want to be sure ... Well if you are missing frames it is difficult to fix it! But using -timestep indeed allows you to change it. Just make sure this is only a due to starting time and not something else. This would matter if you look at time dependent stuff ... Timesteps at t=21610 don't match (8, 10) 8 and 10 and the different time intervals it found not matching. Reading frame 50 time 21670.002 Timesteps at t=21700 don't match (10, 2) Timesteps at t=21702 don't match (2, 8) Timesteps at t=21710 don't match (8, 10) Reading frame 60 time 21760.002 Timesteps at t=21800 don't match (10, 2) On Fri, May 2, 2008 at 1:57 PM, Xavier Periole [EMAIL PROTECTED] wrote: You probably fond the problem. trjcat expects 10 ps intervals between frames. If it is not the case it complains. On Fri, 2 May 2008 13:14:07 +0200 maria goranovic [EMAIL PROTECTED] wrote: I have gmxchecked my individual trr files. They should contain 10 frames each, but the output looks like: # Reading frame 10 time 10002.000 Timesteps at t=1 don't match (10, 2) Last frame 10 time 10002.000 Item#frames Step11 Time11 Lambda 11 Coords 11 Velocities 11 Forces 0 Box 11 gcq#54: I'm a Wishbone and I'm Breaking (Pixies) # I think I have some idea of what the problem might be. I use the following method to continue my simulation trajectories: From the minimized structure, I first run a short 2 ps (1000 step) simulation where I assign initial velocities. I obtain out-1.trr and out-1.edr and out-1.gro. I then want to use tpbconv to continue the simulation, like so: tpbconv -f out-1.trr -s out-1.tpr -e out-1.edr -extend 100 -o out-2.tpr However, out-1.tpr cannot be used to continue the simulation, because new velocities would be assigned, and I might want to change some parameter (like removing restraints) when I continue the simulation. So, I then make a new out-1.tpr file based on a dummy .mdp file, which contains all the new parameters for the continuation run, and which looks like: grompp -f dummy.mdp -c out-1.gro -p temp.top -o out-1.tpr ### integrator = md tinit = 0 init_step = 1000 nsteps = 0 dt = 0.002 etc... ### So, the new tpr file suggests that the simulation should start from 1000x 0.002 = 2 ps. This seems to be the source of the problem somehow, because the error when I use gmxcheck on the merger trajectory is typically like: Timesteps at t=21702 don't match (2, 8) So, there seems to be a 2 ps offset. the above output is also not very clear to me. What does (2,8) mean ? I hope this makes things a little more clearer. So there are no missing frames, but how do I fix the timestamps and so ? Thanks a lot for reading the long email and helping out -maria On Fri, May 2, 2008 at 12:25 PM, Xavier Periole [EMAIL PROTECTED] wrote: On Fri, 2 May 2008 12:01:37 +0200 maria goranovic [EMAIL PROTECTED] wrote: I used: trjcat -o out.trr -f *trr It looks like you have missing frames in your xtc files ... that happens sometimes when the simulation is stopped and restarted from the trr file whereas the buffer of the xtc file is not emptied. Did you gmxcheck the xtc files? On Fri, May 2, 2008 at 11:42 AM, Mark Abraham [EMAIL PROTECTED] wrote: maria goranovic wrote: Hi, After using gmxcheck on a merged trajectory, I get the following error throughout the trajectory. What does this mean ? How did you merge the trajectory? Thank you for the help. . Timesteps at t=21610 don't match (8, 10) Reading frame 50 time 21670.002 Timesteps at t=21700 don't match (10, 2) Timesteps at t=21702 don't match (2, 8) Timesteps at t=21710 don't match (8, 10) Reading frame 60 time 21760.002 Timesteps at t=21800 don't match (10, 2
[gmx-users] hydrogen bonds of peptide with lipids
Dear All, Where are the donor and acceptor atoms defined for the g_hbond analysis ? I was trying to calculate h-bonds between a peptide and a popc bilayer, but there are no acceptor or donors listed for POPC. How can one change this ? Sincerely, -Maria -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] hydrogen bonds of peptide with lipids
Yes, I looked into that. But could not find any information about how to include new acceptor or donor atoms. Could you please be more specific ? Thank you ! On Thu, Apr 17, 2008 at 12:34 PM, Justin A. Lemkul [EMAIL PROTECTED] wrote: Quoting maria goranovic [EMAIL PROTECTED]: Dear All, Where are the donor and acceptor atoms defined for the g_hbond analysis ? I was trying to calculate h-bonds between a peptide and a popc bilayer, but there are no acceptor or donors listed for POPC. How can one change this ? Have a look at g_hbond -h -Justin Sincerely, -Maria -- Maria G. Technical University of Denmark Copenhagen Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] hydrogen bonds of peptide with lipids
Yes, I am using united atoms. I am looking for H-bonds between phosphate groups of lipids and the H-bonding atoms of the protein. i have used g_hbond to find the relevant intra-protein H-bonds, but need to find protein-lipid H-bonds. I tried using g_hbond, using the protein and POPC as the two groups, but g_hbond does not detect any acceptor or donor atoms in POPC, because I get something like: = Calculating hydrogen bonds between SideChain_ARG_12 (12 atoms) and POPC (17524 atoms) Found 3 donors and 3 acceptors = So, the question is: where are the listings for acceptor and donor atoms for using g_hbond I hope this clarifies issues. Thank you -Maria On Thu, Apr 17, 2008 at 5:11 PM, [EMAIL PROTECTED] wrote: Are you using united atom lipids? If so, you may want to reconsider attempting this. If not, you'll be more likely to get further assistance if you provide quite a bit more information and demonstrate that you invested some time trying to solve this. -- original message -- Yes, I looked into that. But could not find any information about how to include new acceptor or donor atoms. Could you please be more specific ? Thank you ! On Thu, Apr 17, 2008 at 12:34 PM, Justin A. Lemkul [EMAIL PROTECTED] wrote: [Hide Quoted Text] Quoting maria goranovic [EMAIL PROTECTED]: Dear All, Where are the donor and acceptor atoms defined for the g_hbond analysis ? I was trying to calculate h-bonds between a peptide and a popc bilayer, but there are no acceptor or donors listed for POPC. How can one change this ? Have a look at g_hbond -h -Justin Sincerely, -Maria -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] bilayer simulation crashes after 2 ns or 7 ns of stable runs. why does system explode
Hi, Sorry for the incomplete details. Here they are now: I started with a well-equilibrated POPC bilayer, and changed one POPC lipid to a lipid of my interest. I wrote the topology file for the new lipid accordingly. After that, I did some simple steepest descent minimization, and followed it up by dynamics. Here is the .mdp file for the runs. There is a preceding 25,000-step simulation where the initial velocities are assigned. The mdp file below is what is being used for equilibrium dynamics. thank you for the suggestions. I will also explore the archives ; ; Input file ; ;- ; BASICS ;- title = dummy-file cpp = /usr/bin/cpp integrator = md tinit = 0 init_step = 25000 nsteps = 10 dt = 0.002 ;- ; BOND PARAMETERS ;- constraints = hbonds constraint_algorithm = lincs unconstrained_start = yes lincs_order = 4 lincs_warnangle = 30 ;- ; OUTPUT CONTROL ;- nstxout = 5000 ; positions nstvout = 5000 ; velocity nstlog = 5000 ; energies to log file nstenergy = 5000 ; energy to energy file ;- ; MISCELLANEOUS ;- comm_mode = linear nstlist = 10 ns_type = grid pbc = xyz ; -- ; NONBONDED INTERACTIONS ; -- coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rlist = 1.0 rvdw= 1.0 fourierspacing = 0.1 pme_order = 4 ewald_rtol = 1e-5 ; --- ; NPT ; --- Tcoupl = berendsen tc-grps = LIP Solvent tau_t = 0.1 0.1 ref_t = 313.0313.0 Pcoupl = berendsen Pcoupltype = semiisotropic tau_p = 1.01.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.01.0 ; --- gen_vel = no ; --- On Fri, Apr 4, 2008 at 6:44 PM, Justin A. Lemkul [EMAIL PROTECTED] wrote: Quoting Justin A. Lemkul [EMAIL PROTECTED]: Quoting maria goranovic [EMAIL PROTECTED]: Dear All I am running a 128-lipid bilayer simulation with standard parameters. The simulation abruptly crashed after 2 ns, and a look into the pdb files suggested that bonds were being broken and eventually the lipids explode. I tried increasing the cutoffs from 1.0 to 1.4, and this time also, the simulation exploded, but at a different time point. And as an aside, broken bonds are only a visualization effect; mdrun doesn't write broken molecules. Also, providing your .mdp file would be of use. -Justin The energy remains nice and stable till the explosion. How does one fix this ? What is planting these bombs ? You'll have to describe how you minimized and equilibrated your bilayer before we'll have any idea what's going on. Also have a thorough look through the archives; many users have posted about bilayers exploding (including yours truly). -Justin Thank you for suggestions. -- Maria G. Technical University of Denmark Copenhagen Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] bilayer simulation crashes after 2 ns or 7 ns of stable runs. why does system explode
Dear All I am running a 128-lipid bilayer simulation with standard parameters. The simulation abruptly crashed after 2 ns, and a look into the pdb files suggested that bonds were being broken and eventually the lipids explode. I tried increasing the cutoffs from 1.0 to 1.4, and this time also, the simulation exploded, but at a different time point. The energy remains nice and stable till the explosion. How does one fix this ? What is planting these bombs ? Thank you for suggestions. -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem with bilayer PBC. after dynamics, bilayer becomes 2 monolayers (shift in box center?)
Hello Folks, I am simulations a lipid bilayer. After minimization, the output .gro file contains a bilayer that is a layer of water sandwiched between 2 monolayers of lipids (instead of being the other way around). I guess this has something to do with the periodic shift in boxes or something. Can someone please clarify this for me ? Thank you -Maria -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gromacs slow for 23000 atom DPPC bilayer on a (1 x 4) node: 50 ps in 10 hours
An update: Using a 4th order PME spline resulted in ~ 15 % increase in efficiency. Thank you, Carsten. On Mon, Mar 24, 2008 at 3:08 PM, maria goranovic [EMAIL PROTECTED] wrote: Dear All, My apologies. I had too big a simulation cell, and too few atoms, hence the problem. No particular reason to choose order 5. I will try with pme_order 4 and see if it improves performance anyway. thanks ! -maria On Mon, Mar 24, 2008 at 2:19 PM, Carsten Kutzner [EMAIL PROTECTED] wrote: Am 24.03.2008 um 10:17 schrieb maria goranovic: Hi Folks, My simulation is running too slow. It took 10 wall clock hours (40 cpu hours) for a short 50 ps simulation of a ~ 23000 atom DPPC bilayer. The hardware is a 4-cpu core. The installation is gromacs 3.3.1. I have run much larger systems (~ 16 atoms) using the same gromacs installation on the same hardware, and they run much faster than this (200 ps per 40 cpu hours). Can anybody suggest why this is happening ? Is it because of latency in the cpu communication? If so, what is the workaround ? Is there a special reason for using pme_order=5? I would use the default, 4 instead, or at least an even number. Carsten My .mdp script is below. These are the run commands. grompp -np 4 -v -f heat.mdp -c minim4.gro -p dppc.top -n dppc.ndx -o heat.tpr mpirun -np 4 ~/bin/mdrun_mpi -np 4 -v -s heat.tpr -o heat.trr -c heat.gro -e heat -g heat.log heat.out ;### ; heat.mdp ; title = heating cpp = /usr/bin/cpp constraints = hbonds constraint_algorithm = lincs unconstrained_start = yes integrator = md nsteps = 25000 dt = 0.002 comm_mode = linear nstxout = 5000 nstvout = 5000 nstlog = 5000 nstenergy = 5000 nstlist = 10 ns_type = grid pbc = xyz ; -- coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rlist = 1.0 rvdw= 1.0 fourierspacing = 0.1 pme_order = 5 ewald_rtol = 1e-5 ; --- ; Berendsen temperature and preasure coupling Tcoupl = berendsen tc-grps = DPPC SOL tau_t = 0.6 0.6 ; i have also tried a tau value of 0.1, but no speed up ref_t = 323.0 323.0 Pcoupl = berendsen Pcoupltype = semiisotropic tau_p = 1.01.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.01.0 ; --- gen_vel = yes gen_temp= 323.0 gen_seed= 194040 ;### -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Maria G. Technical University of Denmark Copenhagen -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Gromacs slow for 23000 atom DPPC bilayer on a (1 x 4) node: 50 ps in 10 hours
Hi Folks, My simulation is running too slow. It took 10 wall clock hours (40 cpu hours) for a short 50 ps simulation of a ~ 23000 atom DPPC bilayer. The hardware is a 4-cpu core. The installation is gromacs 3.3.1. I have run much larger systems (~ 16 atoms) using the same gromacs installation on the same hardware, and they run much faster than this (200 ps per 40 cpu hours). Can anybody suggest why this is happening ? Is it because of latency in the cpu communication? If so, what is the workaround ? My .mdp script is below. These are the run commands. grompp -np 4 -v -f heat.mdp -c minim4.gro -p dppc.top -n dppc.ndx -o heat.tpr mpirun -np 4 ~/bin/mdrun_mpi -np 4 -v -s heat.tpr -o heat.trr -c heat.gro -e heat -g heat.log heat.out ;### ; heat.mdp ; title = heating cpp = /usr/bin/cpp constraints = hbonds constraint_algorithm = lincs unconstrained_start = yes integrator = md nsteps = 25000 dt = 0.002 comm_mode = linear nstxout = 5000 nstvout = 5000 nstlog = 5000 nstenergy = 5000 nstlist = 10 ns_type = grid pbc = xyz ; -- coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rlist = 1.0 rvdw= 1.0 fourierspacing = 0.1 pme_order = 5 ewald_rtol = 1e-5 ; --- ; Berendsen temperature and preasure coupling Tcoupl = berendsen tc-grps = DPPC SOL tau_t = 0.6 0.6 ; i have also tried a tau value of 0.1, but no speed up ref_t = 323.0 323.0 Pcoupl = berendsen Pcoupltype = semiisotropic tau_p = 1.01.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.01.0 ; --- gen_vel = yes gen_temp= 323.0 gen_seed= 194040 ;### -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gromacs slow for 23000 atom DPPC bilayer on a (1 x 4) node: 50 ps in 10 hours
Dear All, My apologies. I had too big a simulation cell, and too few atoms, hence the problem. No particular reason to choose order 5. I will try with pme_order 4 and see if it improves performance anyway. thanks ! -maria On Mon, Mar 24, 2008 at 2:19 PM, Carsten Kutzner [EMAIL PROTECTED] wrote: Am 24.03.2008 um 10:17 schrieb maria goranovic: Hi Folks, My simulation is running too slow. It took 10 wall clock hours (40 cpu hours) for a short 50 ps simulation of a ~ 23000 atom DPPC bilayer. The hardware is a 4-cpu core. The installation is gromacs 3.3.1. I have run much larger systems (~ 16 atoms) using the same gromacs installation on the same hardware, and they run much faster than this (200 ps per 40 cpu hours). Can anybody suggest why this is happening ? Is it because of latency in the cpu communication? If so, what is the workaround ? Is there a special reason for using pme_order=5? I would use the default, 4 instead, or at least an even number. Carsten My .mdp script is below. These are the run commands. grompp -np 4 -v -f heat.mdp -c minim4.gro -p dppc.top -n dppc.ndx -o heat.tpr mpirun -np 4 ~/bin/mdrun_mpi -np 4 -v -s heat.tpr -o heat.trr -c heat.gro -e heat -g heat.log heat.out ;### ; heat.mdp ; title = heating cpp = /usr/bin/cpp constraints = hbonds constraint_algorithm = lincs unconstrained_start = yes integrator = md nsteps = 25000 dt = 0.002 comm_mode = linear nstxout = 5000 nstvout = 5000 nstlog = 5000 nstenergy = 5000 nstlist = 10 ns_type = grid pbc = xyz ; -- coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rlist = 1.0 rvdw= 1.0 fourierspacing = 0.1 pme_order = 5 ewald_rtol = 1e-5 ; --- ; Berendsen temperature and preasure coupling Tcoupl = berendsen tc-grps = DPPC SOL tau_t = 0.6 0.6 ; i have also tried a tau value of 0.1, but no speed up ref_t = 323.0 323.0 Pcoupl = berendsen Pcoupltype = semiisotropic tau_p = 1.01.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.01.0 ; --- gen_vel = yes gen_temp= 323.0 gen_seed= 194040 ;### -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] selecting residues which are within cutoff distances
Hello Folks, I have a protein trajectory to analyze. The goal is to find all residues within a 6 Angstrom radius of another residue, and list their names (for example) over a trajectory. How can one do this ? I tried using g_mdmat. However, the eps generated by using xps2pm does not really convey too much perhaps because of bad resolution ? Is there any other way ? Thank you in advance -Maria -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Selection of multiple residues
Hello, I want to select 300 residues out of my 1000 residue protein and make an index out of it. make_ndx does not seem to have a simple method to do this. These are all residues in the same chain. How does one do this ? Sincerely -Maria -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Selection of multiple residues
to select and copy the indices from an existing index-file to create a new group I am sorry I did not understand the meaning of the above ? I will have the first atom number and the last atom number, and then ? How do I copy the indices ... On Fri, Feb 22, 2008 at 10:58 AM, Bjoern Windshuegel [EMAIL PROTECTED] wrote: Hi, I assume you want to select a range of residues, not some scattered amino acids.. So just check from your gro-file the atom numbers of begin and end of the region you need and use the information to select and copy the indices from an existing index-file to create a new group. Best regards, Björn Hello, I want to select 300 residues out of my 1000 residue protein and make an index out of it. make_ndx does not seem to have a simple method to do this. These are all residues in the same chain. How does one do this ? Sincerely -Maria -- Maria G. Technical University of Denmark Copenhagen -- Dr. Björn Windshügel Department of Pharmaceutical Chemistry University of Kuopio P.O. Box 1627 70211 Kuopio, FINLAND Email: [EMAIL PROTECTED] Phone: (+358) 17 162463 Fax: (+358) 17 162456 Web: www.uku.fi/farmasia/fake/modelling/index.shtml ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
