Re: 回复： Re: 回复： Re: [gmx-users ] Is 2D projection in g_anaeig
xi zhao wrote: Dear sir: I am sorry. Can I understand 2D projection = Probability Distributions P(v1,v2) in Proteins 2005; 60:485. How to produce 3D Don't know the paper, but such a projection can give you a probability distribution if you histogram it. plot of P(v1,v2)? how can I look for transit paths from P(v1,v2)? How can I calculate free enery in gromacs using P(v1,v2)? You need three variables to make a three dimensional energy landscape. Use g_sham for this (you can also use other variables there). Thank you in advance! */David van der Spoel [EMAIL PROTECTED]/* 写道： xi zhao wrote: Dear sir : Can I understand 2D projection = Component (PC) Probability Distributions P(v1,v2)? If this is a true, and how to define the Pmax in detail? Thank you in advance! you can specify the vectors you want with -v1 -v2 */Nguyen Hoang Phuong /* 写道： Dear gmx users, Does the 2D projection plot has something to do with convergence of the trajectory? If so, what kind of shape of plot shows the trajectory is non-converged? Normally, I use RMSD plot to see if the trajectory tends to converge. Now my concern is how to see whether trajectory is conserved or not based on 2D projection analyses. Thanks in advance, Linda you can, for example, have a look at the 2D projection of the trajectory onto the first two principal components obtained from the principal component analysis. In this paper Proteins 2005; 60:485 we used this kind of map to check the convergence of the simulation obtained from a replica exchange simulation with the counterpart obtained from high temperature, normal simulation. Phuong ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 雅虎免费邮箱-3.5G容量，20M附件 ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 雅虎免费邮箱-3.5G容量，20M附件 http://cn.mail.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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-3.3.1 installation problem
Chenyue Xing wrote: Hi all, I'm trying to install gromacs-3.3.1. I first installed fftw-3.0.1 with --enable-float and setenv CPPFLAGS and LDFLAGS to my fftw include/ and lib/ directories. ./configure successfully passed all checking (seems so) but it stopped at ' config.status: executing depfiles commands' and didn't print 'Gromacs is ready to compile. Binary and library files are ...' such stuff. If I try to 'make', it'll go into some infinite loop: keep printing sentences from ' /bin/sh ./config.status config.status: creating Makefile' ...to ... 'config.status: src/config.h is unchanged config.status: executing depfiles commands' No matter it's just 'make' or 'make install' or 'make distclean', it only prints the loop of the above 'config.status'. could it be that the machine you are working on has a different time/date than the machine where the files are? (e.g. when using NFS) I'm posting the log of configure so that some experienced users may help me find the error. I appreciate any response! checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... pax checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ANSI C... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking how to run the C preprocessor... cc -E checking whether cc accepts -O3... yes checking whether cc accepts -malign-double... yes checking whether cc accepts -funroll-all-loops... yes checking whether cc accepts -O3 -fomit-frame-pointer -finline-functions -Wall - Wno-unused -malign-double -funroll-all-loops... yes checking whether byte ordering is bigendian... no checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h.. . yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for int... yes checking size of int... 4 checking for long int... yes checking size of long int... 4 checking for long long int... yes checking size of long long int... 8 checking floating-point format... IEEE754 (little-endian byte and word order) checking for a BSD-compatible install... /usr/bin/install -c checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /bin/sed checking for ld used by cc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from cc object... ok checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if cc supports -fno-rtti -fno-exceptions... yes checking for cc option to produce PIC... -fPIC checking if cc PIC flag -fPIC works... yes checking if cc static flag -static works... yes checking if cc supports -c -o file.o... yes checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes configure: creating libtool appending configuration tag CXX to libtool checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC checking if g++ PIC flag -fPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking whether the g++ linker (/usr/bin/ld) supports shared
Re: [gmx-users] comm_mode
[EMAIL PROTECTED] wrote:
Dear users,
There is an option in .mdp named comm_mode, which deals with the transition
and rotation of the molecule being simulated. I want to know why the transition
and rotation happens during the simulation. Can any one suggest me any
reading material where in I can find how the dynamics is performed internally.
thanks in advance
@Article{Harvey98a,
author = {S. C. Harvey and R. K. Z. Tan and T. E. Cheatham},
title = {The flying ice cube: Velocity rescaling in molecular
dynamics leads to violation of energy equipartition},
journal = {J. Comp. Chem.},
year = 1998,
volume = 19,
pages ={726-740}
}
regards
Anwar
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David.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
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Re: [gmx-users] gromacs-3.3.1 installation problem
Hi David, Thanks for your reply. I actually found the time difference (25 min different)between my working machine and the other machine where files are. I'll contact my sysadmin. But as I successfully installed gromacs-3.1 under the same condition, does that mean this problem only occurs on version3.3? Thank you again! Chenyue On 8/13/06, David van der Spoel [EMAIL PROTECTED] wrote: Chenyue Xing wrote: Hi all, I'm trying to install gromacs-3.3.1. I first installed fftw-3.0.1 with --enable-float and setenv CPPFLAGS and LDFLAGS to my fftw include/ and lib/ directories. ./configure successfully passed all checking (seems so) but it stopped at ' config.status: executing depfiles commands' and didn't print 'Gromacs is ready to compile. Binary and library files are ...' such stuff. If I try to 'make', it'll go into some infinite loop: keep printing sentences from ' /bin/sh ./config.status config.status: creating Makefile'...to ... 'config.status: src/config.h is unchanged config.status: executing depfiles commands' No matter it's just 'make' or 'make install' or 'make distclean', it only prints the loop of the above 'config.status'.could it be that the machine you are working on has a differenttime/date than the machine where the files are?(e.g. when using NFS) I'm posting the log of configure so that some experienced users may help me find the error. I appreciate any response! checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... pax checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ANSI C... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking how to run the C preprocessor... cc -E checking whether cc accepts -O3... yes checking whether cc accepts -malign-double... yes checking whether cc accepts -funroll-all-loops... yes checking whether cc accepts-O3 -fomit-frame-pointer -finline-functions -Wall - Wno-unused -malign-double -funroll-all-loops... yes checking whether byte ordering is bigendian... no checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h.. . yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for int... yes checking size of int... 4 checking for long int... yes checking size of long int... 4 checking for long long int... yes checking size of long long int... 8 checking floating-point format... IEEE754 (little-endian byte and word order) checking for a BSD-compatible install... /usr/bin/install -c checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /bin/sed checking for ld used by cc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from cc object... ok checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if cc supports -fno-rtti -fno-exceptions... yes checking for cc option to produce PIC... -fPIC checking if cc PIC flag -fPIC works... yes checking if cc static flag -static works... yes checking if cc supports -c -o file.o... yes checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes configure: creating libtool appending configuration tag CXX to libtool checking for ld used by g++... /usr/bin/ld
Re: [gmx-users] gromacs-3.3.1 installation problem
Chenyue Xing wrote: Hi David, Thanks for your reply. I actually found the time difference (25 min different) between my working machine and the other machine where files are. I'll contact my sysadmin. But as I successfully installed gromacs-3.1 under the same condition, does that mean this problem only occurs on version3.3? no, you probably don't what the time difference was before. you can try to run first configure, then wait 30 minutes and then run make. Thank you again! Chenyue On 8/13/06, *David van der Spoel* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Chenyue Xing wrote: Hi all, I'm trying to install gromacs-3.3.1. I first installed fftw-3.0.1 with --enable-float and setenv CPPFLAGS and LDFLAGS to my fftw include/ and lib/ directories. ./configure successfully passed all checking (seems so) but it stopped at ' config.status: executing depfiles commands' and didn't print 'Gromacs is ready to compile. Binary and library files are ...' such stuff. If I try to 'make', it'll go into some infinite loop: keep printing sentences from ' /bin/sh ./config.status config.status: creating Makefile' ...to ... 'config.status: src/config.h is unchanged config.status: executing depfiles commands' No matter it's just 'make' or 'make install' or 'make distclean', it only prints the loop of the above 'config.status'. could it be that the machine you are working on has a different time/date than the machine where the files are? (e.g. when using NFS) I'm posting the log of configure so that some experienced users may help me find the error. I appreciate any response! checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... pax checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ANSI C... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking how to run the C preprocessor... cc -E checking whether cc accepts -O3... yes checking whether cc accepts -malign-double... yes checking whether cc accepts -funroll-all-loops... yes checking whether cc accepts -O3 -fomit-frame-pointer -finline-functions -Wall - Wno-unused -malign-double -funroll-all-loops... yes checking whether byte ordering is bigendian... no checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h.. . yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for int... yes checking size of int... 4 checking for long int... yes checking size of long int... 4 checking for long long int... yes checking size of long long int... 8 checking floating-point format... IEEE754 (little-endian byte and word order) checking for a BSD-compatible install... /usr/bin/install -c checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /bin/sed checking for ld used by cc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from cc object... ok checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip
[gmx-users] Uncorrelated configurations
Dear Gmx Users I have one trajectory of 800ps. I need extract of this trajectory, only the uncorrelated (statistically independent) configurations. So I need know how many ps separates two consecutive configuratios. Which procedure I can use for this analysis? Thanks eef __Eudes Eterno FiletiCentro de Ciência Naturais e HumanasUniversidade Federal do ABCRua Santa Adélia, 166CEP 09210-170 skype: eefileti ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Uncorrelated configurations
Eudes Fileti wrote: Dear Gmx Users I have one trajectory of 800ps. I need extract of this trajectory, only the uncorrelated (statistically independent) configurations. So I need know how many ps separates two consecutive configuratios. Which procedure I can use for this analysis? what is the definition of correlation in this context? you don't even say what system it is... Thanks eef __ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 CEP 09210-170 skype: eefileti ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] AFM pulling
From: Susanna Hug [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] AFM pulling Date: Mon, 14 Aug 2006 13:23:28 +0200 Hi gmx-users! I am trying to simulate the diffusion of mannitol through a lipid bilayer with AFM pulling. Does someone have a idea, how I can calculate the diffusion coefficent from the potential of mean force? I have some references, but for different methodes like umbrella sampling. AFM pulling is identical to umbrella sampling. (note that you should pull slow enough so the system is in equilibrium) We should merge these two options into one option. Berk. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] entries in ffG53a6nb.itp
dear all// what is the meaning of and the difference between the [ nonbond_params ] and the [ pairtypes ] sections in the ffG53a6nb.itp file? represents the first the normal LJ-params while the latter contains the 1-4 interaction LJ-params? what is the meaning of 'ptype' and 'func' in the tables? thanks a lot// carsten -- dr carsten baldauf biotechnologisches zentrum der tu dresden http://www.biotec.tu-dresden.de/pisabarro http://www.biotec.tu-dresden.de/~carstenb Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html No Software Patents! See http://www.ffii.org/index.en.html ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] contact
Dear gromacs users How can i calculate the number of contacts during the MD trajectory in complex(protein-protein)? best regard __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] AFM pulling
Thanks, that's good to know! Susanna From: Susanna Hug [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] AFM pulling Date: Mon, 14 Aug 2006 13:23:28 +0200 Hi gmx-users! I am trying to simulate the diffusion of mannitol through a lipid bilayer with AFM pulling. Does someone have a idea, how I can calculate the diffusion coefficent from the potential of mean force? I have some references, but for different methodes like umbrella sampling. AFM pulling is identical to umbrella sampling. (note that you should pull slow enough so the system is in equilibrium) We should merge these two options into one option. Berk. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] entries in ffG53a6nb.itp
On Aug 14, 2006, at 2:49 PM, Carsten Baldauf wrote: dear all// what is the meaning of and the difference between the [ nonbond_params ] and the [ pairtypes ] sections in the ffG53a6nb.itp file? represents the first the normal LJ-params while the latter contains the 1-4 interaction LJ-params? Correct. Many forcefields (e.g. opls) only use scaling factors, and then the pairtypes section isn't necessary. what is the meaning of 'ptype' and 'func' in the tables? ptype is particle type, which makes it possible to separate nuclei from bond polarization charges in polarizable force fields. In the standard force fields we only use atoms. The 'func' field is an integer to specify the type of interaction, for instance if a bond is harmonic, cubic, or e.g. morse bond. It is always used even when there is only a single type of interaction (e.g. for position restraints), since we might add new interaction forms in the future. Cheers, Erik ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] histidine (HISB) planarity how about Trp?
Hi everybody, I am also trying G53a6 in my protein simulation and it is observed that TRP is less planar as compared to those in OPLS. The angle distribution of the impropers are calculated to be wider and thus less populated in the equilibrium angle. Would this hint to a problem in the setup or ff? Shirley Berk Hess wrote: From: Anthony Armstrong [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] histidine (HISB) planarity Date: Fri, 11 Aug 2006 17:19:24 -0400 (EDT) I was having problems keeping my histidines planar, and had to manually edit the .top file produced by pdb2gmx in order to fix the problem. I was just wondering if this problem (i.e. incorrect and incomplete improper dihedral records in the top file) is isolated to histidine topologies generated by pdb2gmx using the G53a6 ff parameters or if manual intervention is frequently required for such standard geometries. I'm using Gromacs v3.3. I start with a pdb file of an extended peptide (with planar his) and issue: pdb2gmx -f -ignh -inter 1STN.pdb -o 1STN.gro -p 1STN.top -ff G53a6 whereupon I specify the single histidine to be of type HISB. After: ...puckered... To correct this it was necessary to delete: 32353033 2gi_1 (this auto generated improper was largely responsible for the ring puckering - its removal alone caused much of the problem to be corrected) and to add: 34303533 2gi_1 (which brough the HE2 hydrogen slightly out of plain back into plain) Indeed this is incorrect. Atom number 32 in the improper dihedral should be replaced by 34. The error is caused by a mistake in ffG53a5/6.rtp fro HISB, the line: CE1 ND1 NE2 HD2 gi_1 should be: CE1 ND1 NE2 HE1 gi_1 I have corrected this for the next release. Is it recommended that I look over every record in the topology file? Is this necessary? Thanks. Well, it is always recommended to check to whole topology, as one can never exclude errors. However, for a reasonable sized protein this is a nearly impossible task. The hope is that when the force field files, in this case the building block files, do not change too often and too much and when thousands of users use them (like with Gromacs), errors will be found quickly and files should be reliable. In this case the error stems for the original GROMOS building block file we have used for making the Gromacs rtp files. The previous GROMOS 43 and 45 force fields did not have explicit hydrogens on the carbons in the ring and apparently the improper for one of the new hydrogens was typed incorrectly. All other interactions for all histidine types seem to be correct. Thanks for reporting this error, Berk. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 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] Re: gmx-users Digest, Vol 28, Issue 42
Dear David Actually I posted my doubt in Vol 28, Issue 38. There I detailed more. Anyway, my system is 1 C60 molecule in 1000 ethanol molecules. As said, I need of structures that do not remember the previous one, i.e. that are structural and statistically not correlated. For this, up to now, I have attemped to use the autocorrelation function of the energy and the block averaging process, but I am still uncertain about the results. An interesting option it could be the analyzis of van Hove function, but I dont kwow how calculate them. Bests eef __Eudes Eterno FiletiCentro de Ciência Naturais e HumanasUniversidade Federal do ABCRua Santa Adélia, 166CEP 09210-170 skype: eefileti ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Re: gmx-users Digest, Vol 28, Issue 42
Eudes Fileti wrote: Dear David Actually I posted my doubt in Vol 28, Issue 38. There I detailed more. sorry, I don't memorize it all... Anyway, my system is 1 C60 molecule in 1000 ethanol molecules. As said, I need of structures that do not remember the previous one, i.e. that are structural and statistically not correlated. For this, up to now, I have attemped to use the autocorrelation function of the energy and the block averaging process, but I am still uncertain about the results. An interesting option it could be the analyzis of van Hove function, but I dont kwow how calculate them. You probably want to know a characteristic interaction time between the C60 and ethanol. Since this will be dominated by Van der Waals interactions you can try to compute the autocorrelation time of C60 - Ethanol-Carbon contacts (using the CVS version of g_hbond) and then use something on that order of time. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] The file
HI! I have a problem. I am working with a molecule that will count two clusters, co-ordinated for cysteins. But in the pdb file does not exist linkings between iron atoms and of the cystens, even so literature affirms that it exists. How I can edit this file? Therefore when I edited it even so it has if visualized the linkings in this format (pdb), when processing it with pdb2gmx the linkings betweenirons and atoms SG of the cisteínas these linkings do not appear in the topology archive. What it can be? E, Silva ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] The file
Elias santos wrote: HI! I have a problem. I am working with a molecule that will count two clusters, co-ordinated for cysteins. But in the pdb file does not exist linkings between iron atoms and of the cystens, even so literature affirms that it exists. How I can edit this file? Therefore when I edited it even so it has if visualized the linkings in this format (pdb), when processing it with pdb2gmx the linkings between irons and atoms SG of the cisteínas these linkings do not appear in the topology archive. What it can be? such clusters are not supported out of the box. you will have to make your own. chapter 5 in the manual. E, Silva ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] renumtop
Dear users Where I can find renumtop thank you prabhakaran ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] nr2nametop
Dear users whwre I can get nr2nametop also and mainly renumtop thank you Prabhakaran ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Sigh . . . Protonating PDB for PRODRG
Hey all, I'm trying to import energy minimization files into VMD to view and I'm getting some errors. First I note that: small molecule pdb file shows a total of 48 atoms my new molecule topology (*.itp file, and *.gro file) show 22 atoms, which I thought were non-H atoms My tally of non-H atoms show 21 non-H atoms (16 C's, 4 O's, and 1 N)-What's going on here? My *.ndx file shows 22 atoms I ran grompp and make_ndx using the small molecule gro and itp files generated by PRODRG. Obviously I lost H's when processing the original pdb file in PRODRG (RTM). When reviewing PRODRG website I saw one can use the ADDhyd [atomname] to the input drawing file, but seeing as HETATM already designates the hydrogen this doesn't make sense. In any case, how do I add more than one H to an atom (e.g. methyl group CH2, CH3)? Where do I place these statements in the file? Last, if the input file to PRODRG is fixed, will this allow VMD to run? Any specific examples or guidance on how to protonate atoms in .pdb files would be greatly appreciated. Regards, Marc ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
