[gmx-users] still can not run md for creatine
Dear All, I still have troubles of starting running md for creatine. For which I created topology using PRODRG programm. The only difference between creatine.top and creating.itp is that creatine top has additional lines: #include ffgmx.itp #include creatine.itp Also please can you tell me where can I get ffgmx.itp file? By trying to run md I am getting an error: Fatal error: moleculetype UNK is redefined Yours sincerely, Olga -- 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] still can not run md for creatine
On 15/11/2010 8:45 PM, Olga Ivchenko wrote: Dear All, I still have troubles of starting running md for creatine. For which I created topology using PRODRG programm. The only difference between creatine.top and creating.itp is that creatine top has additional lines: #include ffgmx.itp #include creatine.itp That won't work because you effectively have the same contents twice. See http://www.gromacs.org/Documentation/Include_File_Mechanism Also please can you tell me where can I get ffgmx.itp file? You probably don't want to. ffgmx has been deprecated for most of a decade. Use the PRODRG 2.5 beta server that will generate a GROMACS-compatible topology file. Other suggestions for other force fields may be found in step 5 of http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation?highlight=Swissparam. You should choose the forcefield based on what you want to observe, rather than by what is available for the first tool that comes to hand. By trying to run md I am getting an error: Fatal error: moleculetype UNK is redefined Yep, you have the same contents twice. Hence redefined 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
Re: [gmx-users] PGI link error: unknown switch --rpath attempted static link of dynamic object fftw/lib/libfftw3.so
Hi, I want to build an all static library because a job running on background nodes may not be able to find the dynamic libraries installed on the front node in my system. My configure line for GCC is: ./configure --prefix=/path-to/gromacs_4.5.3 --enable-mpi --enable-double CC=cc CFLAGS=-O3 MPICC=cc Here I use cc for both C compiler and MPI compiler because it is the name of the C compiler wrapper used on my system which is also functioning for the MPI C compiler. The fftw library is pre-installed on my system which is managed by the Modules package. When loaded, the fftw module sets the environment variables as: prepend-path LD_LIBRARY_PATH /opt/fftw/3.2.2.1/lib setenv FFTW_POST_LINK_OPTS -L/opt/fftw/3.2.2.1/lib -Wl,-rpath=/opt/fftw/3.2.2.1/lib -lfftw3 -lfftw3f setenv FFTW_INCLUDE_OPTS -I/opt/fftw/3.2.2.1/include setenv FFTW_DIR /opt/fftw/3.2.2.1/lib setenv FFTW_INC /opt/fftw/3.2.2.1/include In make, the link line causing the libfftw3 error is: cc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2 -I../../include -DGMXLIBDIR=\/usr/local/packages/nag/GROMACS/phase2b_4.5.3/share/top\ -O3 -MT grompp.o -MD -MP -MF .deps/grompp.Tpo -c -o grompp.o grompp.c mv -f .deps/grompp.Tpo .deps/grompp.Po /bin/sh ../../libtool --tag=CC --mode=link cc -O3 -o grompp grompp.o libgmxpreprocess_mpi_d.la ../mdlib/libmd_mpi_d.la ../gmxlib/libgmx_mpi_d.la -lnsl -lm cc -O3 -o grompp grompp.o ./.libs/libgmxpreprocess_mpi_d.a /usr/local/packages/nag/GROMACS/gromacs-4.5.3/src/mdlib/.libs/libmd_mpi_d.a ../mdlib/.libs/libmd_mpi_d.a /opt/fftw/3.2.2.1/lib/libfftw3.so /usr/lib64/libxml2.so -lz /usr/local/packages/nag/GROMACS/gromacs-4.5.3/src/gmxlib/.libs/libgmx_mpi_d.a ../gmxlib/.libs/libgmx_mpi_d.a -ldl -lnsl -lm -Wl,--rpath -Wl,/opt/fftw/3.2.2.1/lib -Wl,--rpath -Wl,/opt/fftw/3.2.2.1/lib /opt/cray/xt-asyncpe/3.7.24/bin/cc: INFO: linux target is being used /usr/bin/ld: attempted static link of dynamic object `/opt/fftw/3.2.2.1/lib/libfftw3.so' collect2: ld returned 1 exit status GCC doesn't support the -rpath flag but it seems not a problem here. The fftw library has the static and dynamic libraries provided. The linker picks the libfftw3.so. This may be relevant to the specification in the libfftw3.la: # libfftw3.la - a libtool library file # Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-4 # # Please DO NOT delete this file! # It is necessary for linking the library. # The name that we can dlopen(3). dlname='libfftw3.so.3' # Names of this library. library_names='libfftw3.so.3.2.4 libfftw3.so.3 libfftw3.so' # The name of the static archive. old_library='libfftw3.a' # Linker flags that can not go in dependency_libs. inherited_linker_flags=' -pthread' # Libraries that this one depends upon. dependency_libs=' -lm' # Names of additional weak libraries provided by this library weak_library_names='' # Version information for libfftw3. current=5 age=2 revision=4 # Is this an already installed library? installed=yes # Should we warn about portability when linking against -modules? shouldnotlink=no # Files to dlopen/dlpreopen dlopen='' dlpreopen='' # Directory that this library needs to be installed in: libdir='/opt/fftw/3.2.2.1/lib' Is there any workaround to instruct the linker to use the static libfftw3.a? Thanks, Yudong Roland Schulz wrote, On 12/11/2010 18:53: Little bit more background/context would help. Do you try to compile an all static library? If so you of course need a static library of fftw. If it is not all static it normally should accept the dynamic fftw. Then please give us the full configure line, the gcc command line of the link step and the full error message. Roland On Fri, Nov 12, 2010 at 12:17 PM, Yudong Sun yud...@nag.co.uk mailto:yud...@nag.co.uk wrote: Mark Abraham wrote, On 12/11/2010 17:02: On 13/11/2010 3:15 AM, Yudong Sun wrote: Hi, I have some troubles when compiling GROMACS 4.5.3 using PGI compiler on the -rpath flag and also a static link to dynamic libfftw3.so. I use the pre-installed FFTW 3.2.2.1 library on my Linux system. The FFTW library is managed by the Modules package. The fftw module automatically sets the environ variable as: FFTW_POST_LINK_OPTS = -L/opt/fftw/3.2.2.1/lib http://3.2.2.1/lib -Wl,-rpath=/opt/fftw/3.2.2.1/lib http://3.2.2.1/lib -lfftw3 -lfftw3f So how does configure use this information? (hint: providing the configure command line is essential for us to understand any context!) When compiling, an error occurs on the -rpath: pgcc -fast -o grompp grompp.o ./.libs/libgmxpreprocess_mpi_d.a /usr/local/packages/nag/GROMACS/gromacs-4.5.3/src/mdlib/.libs/libmd_mpi_d.a ../mdlib/.libs/libmd_mpi_d.a
[gmx-users] bitinilated peptide
Hi everybody, I would like to submit a biotinilated peptide to MD with 53a6 force field. Do you know where I can look for the topology and parameters file? thank you in advance -- 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] bitinilated peptide
Gloria Saracino wrote: Hi everybody, I would like to submit a biotinilated peptide to MD with 53a6 force field. Do you know where I can look for the topology and parameters file? I would start with a literature search, then the Users' Contribution section of the Gromacs site, then perhaps poke around Google. If nothing turns up, then you've got a long road of parameterization ahead of you. http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin thank you in advance -- 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
Re: [gmx-users] Freeze Groups in Gromacs 4.5.x (bug?)!!!
Dear Mark, users and developers... Indeed, the source of the problems comes from both the constraints and the pressure bath. The temperature bath did not seem to interfere. Now, the problem is clear, to remove constraints is not only compulsory but also recommendable for such simulations. However, the pressure bath (which is the major source of the problems) should not play such a role. This is a limitation of the current implementation of GROMACS or just a plain BUG. I think most people would agree that one should not be limited to NVT simulations when using freeze groups. A previous version (3.2.1) that we have been using in our group was completely immune to both pressure bath and constraints when simulating a frozen protein in water. As far as I remember, this older version did a normal step integration with all its requisites and, in the end, just took back the previous positions for the frozen group (protein). My question remains... Will we be able to use freeze groups together with a NPT simulation in Gromacs 4.5.x??? Any comments from the developers are welcome... Regards, Miguel On 11/11/2010 1:07 AM, Mark Abraham wrote: On 11/11/2010 3:14 AM, Miguel Machuqueiro wrote: Dear users and developers, In GROMACS 4.5.x when using freeze groups on a Protein in a Protein+Solvent system, I noticed that the coordinates of a few atoms (not many, but a few) are changed after a short period of MD (~0.2 ps). Of course, this is wrong! Are there any options in MDP/GROMPP/MDRUN that can be originating this? Or it is some bug in the code? A copy of my input file follows below. Note that this version of GROMACS crashes if one uses constraints in LINCS together with freeze groups. Hence the constraints = none line. Indeed, because imposing the constraints can perturb the (frozen) positions slightly, leading to numerical issues... Similarly, if you couple the frozen groups to a heat bath, you're going to find that they're not actually frozen. And pressure-coupling is not known to always play nicely with frozen groups either (search the archive for more). Any help is appreciated. Regards, Miguel _ ; Input file ; title = zzz cpp = /lib/cpp define = integrator = md tinit = 0.0 dt = 0.002; ps ! nsteps = 100 nstcomm = 10 nstxtcout = 500 xtc-precision = 1000 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 0 nstenergy = 500 nstcalcenergy = 10 ns_type = grid coulombtype = Generalized-Reaction-Field nstlist = 5 rlist = 0.8 rcoulomb= 1.4 epsilon_rf = 54.0 rvdw= 1.4 vdwtype = cut-off ; Energy monitoring energygrps = Protein SOL Tcoupl = v-rescale tc-grps = Protein SOL tau_t = 0.10 0.10 ref_t = 310.0 310.0 ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; lincs_order value of 8 works better than 4 constraint_algorithm=lincs lincs_order = 8 constraints = none lincs-warnangle = 90 freezegrps = Protein freezedim = Y Y Y energygrp_excl = Protein Protein -- Miguel Machuqueiro Department of Chemistry and Biochemistry Faculty of Sciences, University of Lisbon Campo Grande, Edifício C8 (sala 8.5.47) 1149-016 Lisboa, Portugal Tel. : +351 217500112 (int.ext.28547) Mobile: +351 967562285 E-mail: machuque at fc.ul.pt www1: http://webpages.fc.ul.pt/~mamachuqueiro www2: http://cqb.fc.ul.pt/intheochem __ -- 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_sas and g_rdf
Hi everyone, I'm trying to look at the radial distribution function of water around the surface of my protein. For that, I calculated the surface area per residue (g_sas -or). Since I didn't find in the litterature any criteria to choose a minimum area value to count a residue as a a surface residue, I chose to analyze the residues that have an area value 1.3 nm2 I counted 23 residues that have area values 1.3 nm2 I made an index file with one index group for each residue and on index group for SOL_OW Then I ran g_rdf on my trajectory g_rdf -s .tpr -f .xtc -n .ndx -o rdf.xvg -bin 0.02 -com I chose: reference group=the residue I want to analyze group = SOL_OW even though I'm analyzing the residues that have large surface area values, my RDF plot doesn't look like what I was execting: it means an RDF plot with a peak at g(r)=2 or 3 then a decrease in g(r) and finally a g(r)=1 My peak is at g(r)=0.7 and then it increases to g(r)=1 Does anyone have an idea why I have this kind of plot? Because I didn't find any answers in the mailing list. Thank you, Carla -- 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] Extracting protein plus a shell of water from a .xtc file
Dear gmx-users, I'm trying to extract a protein plus a shell of water of a given radius from the .xtc and .gro files obtained from a simulation step. My purpose is to make a second box, smaller then the first, with the protein and the shell of solvent in order to optimize the performance of the simulations that I'm running (they require an incredible amount of time due to the high number of H2O molecules in the box) and retain the data obtained till now without starting a new run from the beginning. I've tried to use trjorder with the command -o .pdb -nshell .xvg -r x.x and I've obtained a .pdb file with the distances of the molecules of water from the protein (reference group: Protein, group of molecules to be ordere: SOL) printed in the B-factor field. Now I'm going to modify the pdb file removing all the molecules that are too far from the protein. I will use this file to make a second box, add the water needed to fill it and restart the simulation. I'm concerned about this procedure because I'm afraid that I'll introduce some errors in the new run, so I wonder if there's a faster way to achieve the same result. I've tried different ways, even using other softwares (e.g: MolMol), but I have not been able to extract the shell of water. If there's no other way to do this, could someone please give me a hint about the procedure I'm attempting on? Thanks in advance for your attention and patience. -- Paolo -- 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: still can not run md for creatine
Hey, Olga - Also please can you tell me where can I get ffgmx.itp file? /$gromacs_folder/share/gromacs/top/ffgmx.itp as well as all other standard topology files are there. By trying to run md I am getting an error: Fatal error: moleculetype UNK is redefined Please post you top and itp files here. Looks like you have 2 creatine molecules in your topology right now. Good luck! Vitaly I still have troubles of starting running md for creatine. For which I created topology using PRODRG programm. The only difference between creatine.top and creating.itp is that creatine top has additional lines: #include ffgmx.itp #include creatine.itp Also please can you tell me where can I get ffgmx.itp file? By trying to run md I am getting an error: Fatal error: moleculetype UNK is redefined -- 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: still can not run md for creatine
Hey Vitaly, Thank you for your reply. Here is the files: *itp:* ; ; ; This file was generated by PRODRG version AA081006.0504 ; PRODRG written/copyrighted by Daan van Aalten ; and Alexander Schuettelkopf ; ; Questions/comments to d...@davapc1.bioch.dundee.ac.uk ; ; When using this software in a publication, cite: ; A. W. Schuettelkopf and D. M. F. van Aalten (2004). ; PRODRG - a tool for high-throughput crystallography ; of protein-ligand complexes. ; Acta Crystallogr. D60, 1355--1363. ; ; [ moleculetype ] Name nrexcl DRG 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OM 1 DRG OXT 1 -0.701 15.9994 2 C 1 DRG C 10.402 12.0110 3OM 1 DRG O 1 -0.701 15.9994 4 CH2 1 DRG CA 20.185 14.0270 5 N 1 DRG N 20.468 14.0067 6 CH3 1 DRG CAG 20.201 15.0350 7 C 1 DRG CAH 20.377 12.0110 8NZ 1 DRG NAE 2 -0.163 14.0067 9 H 1 DRG HA6 20.023 1.0080 10 H 1 DRG HAE 20.024 1.0080 11NZ 1 DRG NAD 2 -0.163 14.0067 12 H 1 DRG HA5 20.024 1.0080 13 H 1 DRG HAD 20.024 1.0080 [ bonds ] ; ai aj fuc0, c1, ... 2 1 20.125 1340.00.125 1340.0 ; C OXT 2 3 20.125 1340.00.125 1340.0 ; CO 2 4 20.153 715.00.153 715.0 ; C CA 5 4 20.147 871.00.147 871.0 ; N CA 5 6 20.147 871.00.147 871.0 ; N CAG 5 7 20.134 1050.00.134 1050.0 ; N CAH 7 8 20.134 1050.00.134 1050.0 ; CAH NAE 7 11 20.134 1050.00.134 1050.0 ; CAH NAD 8 9 20.100 1870.00.100 1870.0 ; NAE HA6 8 10 20.100 1870.00.100 1870.0 ; NAE HAE 11 12 20.100 1870.00.100 1870.0 ; NAD HA5 11 13 20.100 1870.00.100 1870.0 ; NAD HAD [ pairs ] ; ai aj fuc0, c1, ... 1 5 1 ; OXTN 2 6 1 ; C CAG 2 7 1 ; C CAH 3 5 1 ; ON 4 8 1 ;CA NAE 4 11 1 ;CA NAD 5 9 1 ; N HA6 5 10 1 ; N HAE 5 12 1 ; N HA5 5 13 1 ; N HAD 6 8 1 ; CAG NAE 6 11 1 ; CAG NAD 8 12 1 ; NAE HA5 8 13 1 ; NAE HAD 9 11 1 ; HA6 NAD 10 11 1 ; HAE NAD [ angles ] ; ai aj ak fuc0, c1, ... 1 2 3 2126.0 770.0126.0 770.0 ; OXTC O 1 2 4 2117.0 635.0117.0 635.0 ; OXTC CA 3 2 4 2117.0 635.0117.0 635.0 ; OC CA 2 4 5 2109.5 520.0109.5 520.0 ; C CA N 4 5 6 2121.0 685.0121.0 685.0 ;CAN CAG 4 5 7 2122.0 700.0122.0 700.0 ;CAN CAH 6 5 7 2117.0 635.0117.0 635.0 ; CAGN CAH 5 7 8 2120.0 670.0120.0 670.0 ; N CAH NAE 5 7 11 2120.0 670.0120.0 670.0 ; N CAH NAD 8 7 11 2120.0 670.0120.0 670.0 ; NAE CAH NAD 7 8 9 2120.0 390.0120.0 390.0 ; CAH NAE HA6 7 8 10 2120.0 390.0120.0 390.0 ; CAH NAE HAE 9 8 10 2120.0 445.0120.0 445.0 ; HA6 NAE HAE 7 11 12 2120.0 390.0120.0 390.0 ; CAH NAD HA5 7 11 13 2120.0 390.0120.0 390.0 ; CAH NAD HAD 12 11 13 2120.0 445.0120.0 445.0 ; HA5 NAD HAD [ dihedrals ] ; ai aj ak al fuc0, c1, m, ... 2 1 3 4 2 0.0 167.40.0 167.4 ; imp C OXT O CA 5 4 6 7 2 0.0 167.40.0 167.4 ; imp N CA CAG CAH 7 5 8 11 2 0.0 167.40.0 167.4 ; imp CAHN NAE NAD 8 7 10 9
[gmx-users] Re: Freeze Groups in Gromacs 4.5.x (bug?)!!!
Hey, Miguel - Hmm... I think, frozen particles will give unnatural pressure of your system, that's why barostats do not do their jobs as expected. Maybe it could be interesting to rescale the coordinates of the frozen atoms with the box vectors (with certain corrections in pressure calculation)... but it should be another keyword to control such trick. -- Dr. Vitaly Chaban University of Rochester Indeed, the source of the problems comes from both the constraints and the pressure bath. The temperature bath did not seem to interfere. Now, the problem is clear, to remove constraints is not only compulsory but also recommendable for such simulations. However, the pressure bath (which is the major source of the problems) should not play such a role. This is a limitation of the current implementation of GROMACS or just a plain BUG. I think most people would agree that one should not be limited to NVT simulations when using freeze groups. A previous version (3.2.1) that we have been using in our group was completely immune to both pressure bath and constraints when simulating a frozen protein in water. As far as I remember, this older version did a normal step integration with all its requisites and, in the end, just took back the previous positions for the frozen group (protein). My question remains... Will we be able to use freeze groups together with a NPT simulation in Gromacs 4.5.x??? Any comments from the developers are welcome... Regards, Miguel On 11/11/2010 1:07 AM, Mark Abraham wrote: On 11/11/2010 3:14 AM, Miguel Machuqueiro wrote: Dear users and developers, In GROMACS 4.5.x when using freeze groups on a Protein in a Protein+Solvent system, I noticed that the coordinates of a few atoms (not many, but a few) are changed after a short period of MD (~0.2 ps). Of course, this is wrong! Are there any options in MDP/GROMPP/MDRUN that can be originating this? Or it is some bug in the code? A copy of my input file follows below. Note that this version of GROMACS crashes if one uses constraints in LINCS together with freeze groups. Hence the constraints = none line. Indeed, because imposing the constraints can perturb the (frozen) positions slightly, leading to numerical issues... Similarly, if you couple the frozen groups to a heat bath, you're going to find that they're not actually frozen. And pressure-coupling is not known to always play nicely with frozen groups either (search the archive for more). Any help is appreciated. Regards, Miguel -- 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: still can not run md for creatine
Olga - What is gromos43a1.ff? I do not remember the files with ff-extension in gromacs. I am sure you should include the topology files in the inverse order as compared to what is below: 1) general FF with atoms, bonds, angles, etc (~ include gromos43a1.ff); 2) molecule definition, its own atoms, bonds, etc (~ include creatine.itp) After that, you'll probably get another error, and it will be more informative. Good luck! Vitaly On Mon, Nov 15, 2010 at 12:09 PM, Olga Ivchenko olga.ivche...@gmail.com wrote: Hey Vitaly, Thank you for your reply. Here is the files: itp: ; ; ; This file was generated by PRODRG version AA081006.0504 ; PRODRG written/copyrighted by Daan van Aalten ; and Alexander Schuettelkopf ; ; Questions/comments to d...@davapc1.bioch.dundee.ac.uk ; ; When using this software in a publication, cite: ; A. W. Schuettelkopf and D. M. F. van Aalten (2004). ; PRODRG - a tool for high-throughput crystallography ; of protein-ligand complexes. ; Acta Crystallogr. D60, 1355--1363. ; ; [ moleculetype ] Name nrexcl DRG 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 OM 1 DRG OXT 1 -0.701 15.9994 2 C 1 DRG C 1 0.402 12.0110 3 OM 1 DRG O 1 -0.701 15.9994 4 CH2 1 DRG CA 2 0.185 14.0270 5 N 1 DRG N 2 0.468 14.0067 6 CH3 1 DRG CAG 2 0.201 15.0350 7 C 1 DRG CAH 2 0.377 12.0110 8 NZ 1 DRG NAE 2 -0.163 14.0067 9 H 1 DRG HA6 2 0.023 1.0080 10 H 1 DRG HAE 2 0.024 1.0080 11 NZ 1 DRG NAD 2 -0.163 14.0067 12 H 1 DRG HA5 2 0.024 1.0080 13 H 1 DRG HAD 2 0.024 1.0080 [ bonds ] ; ai aj fu c0, c1, ... 2 1 2 0.125 1340.0 0.125 1340.0 ; C OXT 2 3 2 0.125 1340.0 0.125 1340.0 ; C O 2 4 2 0.153 715.0 0.153 715.0 ; C CA 5 4 2 0.147 871.0 0.147 871.0 ; N CA 5 6 2 0.147 871.0 0.147 871.0 ; N CAG 5 7 2 0.134 1050.0 0.134 1050.0 ; N CAH 7 8 2 0.134 1050.0 0.134 1050.0 ; CAH NAE 7 11 2 0.134 1050.0 0.134 1050.0 ; CAH NAD 8 9 2 0.100 1870.0 0.100 1870.0 ; NAE HA6 8 10 2 0.100 1870.0 0.100 1870.0 ; NAE HAE 11 12 2 0.100 1870.0 0.100 1870.0 ; NAD HA5 11 13 2 0.100 1870.0 0.100 1870.0 ; NAD HAD [ pairs ] ; ai aj fu c0, c1, ... 1 5 1 ; OXT N 2 6 1 ; C CAG 2 7 1 ; C CAH 3 5 1 ; O N 4 8 1 ; CA NAE 4 11 1 ; CA NAD 5 9 1 ; N HA6 5 10 1 ; N HAE 5 12 1 ; N HA5 5 13 1 ; N HAD 6 8 1 ; CAG NAE 6 11 1 ; CAG NAD 8 12 1 ; NAE HA5 8 13 1 ; NAE HAD 9 11 1 ; HA6 NAD 10 11 1 ; HAE NAD [ angles ] ; ai aj ak fu c0, c1, ... 1 2 3 2 126.0 770.0 126.0 770.0 ; OXT C O 1 2 4 2 117.0 635.0 117.0 635.0 ; OXT C CA 3 2 4 2 117.0 635.0 117.0 635.0 ; O C CA 2 4 5 2 109.5 520.0 109.5 520.0 ; C CA N 4 5 6 2 121.0 685.0 121.0 685.0 ; CA N CAG 4 5 7 2 122.0 700.0 122.0 700.0 ; CA N CAH 6 5 7 2 117.0 635.0 117.0 635.0 ; CAG N CAH 5 7 8 2 120.0 670.0 120.0 670.0 ; N CAH NAE 5 7 11 2 120.0 670.0 120.0 670.0 ; N CAH NAD 8 7 11 2 120.0 670.0 120.0 670.0 ; NAE CAH NAD 7 8 9 2 120.0 390.0 120.0 390.0 ; CAH NAE HA6 7 8 10 2 120.0 390.0 120.0 390.0 ; CAH NAE HAE 9 8
[gmx-users] Parameterization
How to parametrize N-acetyl Glucosamine present in my PDB file with AMBER force field to use in GROMACS. Please suggest some solutions. Thanks -- Yuvraj -- 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] electrostatic interaction
Hello, I want to turn off electrostatic interactions between CH4 and SOL in my system. I am using ffG53a6 forcefield for CH4 and spc for my water model. CH4 is an united atom and so I can't make the charges zero in the topology. Is there any other way I can turn off electrostatic interactions? Thanks. -Nisha -- 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] Parameterization
Dear Yuvraj: There is a protocol to find the charges and force field parameters for new molecules for the AMBER force field. The best way is to try to find the parameters from a publication. If you dont find anything then use RED to find the charges (http://q4md-forcefieldtools.org/RED/). Then use ambertools to find the necessary force field parameters and generate an AMBER topology. After that use acpype to transform the amber topology to a GROMACS topology. From the GROMACS topology the create an itp file to use in your GROMACS TOPOLOGY. To better understand what I said please read the reference for the force field, the GROMACS manual and the RED tutorial. Best Regards, Anthony On Mon, Nov 15, 2010 at 5:13 PM, YUVRAJ UBOVEJA yuvrajthe...@gmail.com wrote: How to parametrize N-acetyl Glucosamine present in my PDB file with AMBER force field to use in GROMACS. Please suggest some solutions. Thanks -- Yuvraj -- gmx-users mailing list gmx-us...@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
Re: [gmx-users] electrostatic interaction
On 16/11/2010 7:14 AM, nishap.pa...@utoronto.ca wrote: Hello, I want to turn off electrostatic interactions between CH4 and SOL in my system. I am using ffG53a6 forcefield for CH4 and spc for my water model. CH4 is an united atom and so I can't make the charges zero in the topology. Is there any other way I can turn off electrostatic interactions? Thanks. -Nisha Use an energy group exclusion. See manual. 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
Re: [gmx-users] Extracting protein plus a shell of water from a .xtc file
On 16/11/2010 2:30 AM, Paolo Conflitti wrote: Dear gmx-users, I'm trying to extract a protein plus a shell of water of a given radius from the .xtc and .gro files obtained from a simulation step. My purpose is to make a second box, smaller then the first, with the protein and the shell of solvent in order to optimize the performance of the simulations that I'm running (they require an incredible amount of time due to the high number of H2O molecules in the box) and retain the data obtained till now without starting a new run from the beginning. I've tried to use trjorder with the command -o .pdb -nshell .xvg -r x.x and I've obtained a .pdb file with the distances of the molecules of water from the protein (reference group: Protein, group of molecules to be ordere: SOL) printed in the B-factor field. Now I'm going to modify the pdb file removing all the molecules that are too far from the protein. I will use this file to make a second box, add the water needed to fill it and restart the simulation. I'm concerned about this procedure because I'm afraid that I'll introduce some errors in the new run, so I wonder if there's a faster way to achieve the same result. I've tried different ways, even using other softwares (e.g: MolMol), but I have not been able to extract the shell of water. If there's no other way to do this, could someone please give me a hint about the procedure I'm attempting on? Thanks in advance for your attention and patience. Since you'll have to re-equilibrate this new water box anyway, why not just take away all the water, and use editconf and genbox to generate the box of the new size? There's no significant advantage to using your waters in the .xtc over those generated by genbox. g_select is a new GROMACS 4.5 tool that is well suited to your approach for solving this problem, but I do not think even its limited complexity is worth while. 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
Re: [gmx-users] Installing mdrun-gpu Using Gromacs-4.5.3
Thank you very much for writing! I have tried what was suggested, and the following errors were produced follow the use of the make mdrun command: [100%] Building C object src/kernel/CMakeFiles/mdrun.dir/md_openmm.c.o Linking CXX executable mdrun-gpu ld: warning: in /usr/local/openmm/lib/libOpenMM.dylib, file was built for i386 which is not the architecture being linked (x86_64) Undefined symbols: OpenMM::Context::~Context(), referenced from: _openmm_cleanup in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) OpenMM::Platform::getDefaultPluginsDirectory(), referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) OpenMM::Context::getState(int) const, referenced from: _openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) OpenMM::MonteCarloBarostat::MonteCarloBarostat(double, double, int), referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) OpenMM::NonbondedForce::getNonbondedMethod() const, referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) OpenMM::Context::setVelocities(std::vectorOpenMM::Vec3, std::allocatorOpenMM::Vec3 const), referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) OpenMM::CustomTorsionForce::CustomTorsionForce(std::basic_stringchar, std::char_traitschar, std::allocatorchar const), referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) OpenMM::NonbondedForce::getCutoffDistance() const, referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) OpenMM::NonbondedForce::setCutoffDistance(double), referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) OpenMM::Platform::getPlatform(int), referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) OpenMM::NonbondedForce::addException(int, int, double, double, double, bool), referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) OpenMM::AndersenThermostat::AndersenThermostat(double, double), referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) OpenMM::Platform::setPropertyDefaultValue(std::basic_stringchar, std::char_traitschar, std::allocatorchar const, std::basic_stringchar, std::char_traitschar, std::allocatorchar const), referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) OpenMM::HarmonicBondForce::addBond(int, int, double, double), referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) OpenMM::State::getPotentialEnergy() const, referenced from: _openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) OpenMM::GBSAOBCForce::setNonbondedMethod(OpenMM::GBSAOBCForce::NonbondedMethod), referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) OpenMM::CustomTorsionForce::addPerTorsionParameter(std::basic_stringchar, std::char_traitschar, std::allocatorchar const), referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) OpenMM::VerletIntegrator::VerletIntegrator(double), referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) OpenMM::Platform::getPropertyNames(), referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) OpenMM::NonbondedForce::NonbondedForce(), referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) OpenMM::GBSAOBCForce::GBSAOBCForce(), referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) OpenMM::NonbondedForce::setEwaldErrorTolerance(double), referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) OpenMM::CustomTorsionForce::addTorsion(int, int, int, int, std::vectordouble, std::allocatordouble const), referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in
Re: [gmx-users] Re: still can not run md for creatine
Just the $0.02 that I always seem to contribute in these types of discussions - the topology you have shown below contains some likely problems. The charges (and massive charge group size) can lead to artifacts. We've got a paper due out soon about the implications of incorrect charges, but I would advise you that this topology should *not* be used for production simulation. You'd be better off spending the time to properly parameterize the molecule rather than run a bunch of simulations and get questionable (at best) or wrong (at worst) results. http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin Olga Ivchenko wrote: Hey Vitaly, Thank you for your reply. Here is the files: *itp:* ; ; ; This file was generated by PRODRG version AA081006.0504 ; PRODRG written/copyrighted by Daan van Aalten ; and Alexander Schuettelkopf ; ; Questions/comments to d...@davapc1.bioch.dundee.ac.uk mailto:d...@davapc1.bioch.dundee.ac.uk ; ; When using this software in a publication, cite: ; A. W. Schuettelkopf and D. M. F. van Aalten (2004). ; PRODRG - a tool for high-throughput crystallography ; of protein-ligand complexes. ; Acta Crystallogr. D60, 1355--1363. ; ; [ moleculetype ] Name nrexcl DRG 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OM 1 DRG OXT 1 -0.701 15.9994 2 C 1 DRG C 10.402 12.0110 3OM 1 DRG O 1 -0.701 15.9994 4 CH2 1 DRG CA 20.185 14.0270 5 N 1 DRG N 20.468 14.0067 6 CH3 1 DRG CAG 20.201 15.0350 7 C 1 DRG CAH 20.377 12.0110 8NZ 1 DRG NAE 2 -0.163 14.0067 9 H 1 DRG HA6 20.023 1.0080 10 H 1 DRG HAE 20.024 1.0080 11NZ 1 DRG NAD 2 -0.163 14.0067 12 H 1 DRG HA5 20.024 1.0080 13 H 1 DRG HAD 20.024 1.0080 [ bonds ] ; ai aj fuc0, c1, ... 2 1 20.125 1340.00.125 1340.0 ; C OXT 2 3 20.125 1340.00.125 1340.0 ; CO 2 4 20.153 715.00.153 715.0 ; C CA 5 4 20.147 871.00.147 871.0 ; N CA 5 6 20.147 871.00.147 871.0 ; N CAG 5 7 20.134 1050.00.134 1050.0 ; N CAH 7 8 20.134 1050.00.134 1050.0 ; CAH NAE 7 11 20.134 1050.00.134 1050.0 ; CAH NAD 8 9 20.100 1870.00.100 1870.0 ; NAE HA6 8 10 20.100 1870.00.100 1870.0 ; NAE HAE 11 12 20.100 1870.00.100 1870.0 ; NAD HA5 11 13 20.100 1870.00.100 1870.0 ; NAD HAD [ pairs ] ; ai aj fuc0, c1, ... 1 5 1 ; OXTN 2 6 1 ; C CAG 2 7 1 ; C CAH 3 5 1 ; ON 4 8 1 ;CA NAE 4 11 1 ;CA NAD 5 9 1 ; N HA6 5 10 1 ; N HAE 5 12 1 ; N HA5 5 13 1 ; N HAD 6 8 1 ; CAG NAE 6 11 1 ; CAG NAD 8 12 1 ; NAE HA5 8 13 1 ; NAE HAD 9 11 1 ; HA6 NAD 10 11 1 ; HAE NAD [ angles ] ; ai aj ak fuc0, c1, ... 1 2 3 2126.0 770.0126.0 770.0 ; OXT CO 1 2 4 2117.0 635.0117.0 635.0 ; OXT C CA 3 2 4 2117.0 635.0117.0 635.0 ; O C CA 2 4 5 2109.5 520.0109.5 520.0 ; C CAN 4 5 6 2121.0 685.0121.0 685.0 ;CAN CAG 4 5 7 2122.0 700.0122.0 700.0 ;CAN CAH 6 5 7 2117.0 635.0117.0 635.0 ; CAGN CAH 5 7 8 2120.0 670.0120.0 670.0 ; N CAH NAE 5 7 11 2120.0 670.0120.0 670.0 ;
Re: [gmx-users] compressing two selections or just the reverse of pulling simulation
Samrat Pal wrote: Hi All, In general what we do in pulling simulations that we pull one selection keeping the other fixed. In that case the distance between the two selections increases with time. Now, I want to push the selections i.e. one selection will be kept fixed and the other will be pushed towards the fixed one so that the distance between the two selection will decrease. Is it possible to do that in GROMACS? What should I modify in the mdp file? I am attaching a mdp file that I have used for pulling simulations (only the pull part). ; pull code pull = umbrella pull_geometry = distance pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = freeze pull_group1 = pull pull_rate1 = 0.01 pull_k1 = 1000 I have used pull_dim N N Y as I am interested to pull only in the z direction. Should I just use N N -Y to do the compressing simulations? You can't specify negative yes for a pulling direction. Instead, just set the pull rate to, i.e., -0.01 to pull in the opposite direction. -Justin Please suggest. Thanks in advance. Samrat -- 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
Re: [gmx-users] Installing mdrun-gpu Using Gromacs-4.5.3
Hi Solomon, [100%] Building C object src/kernel/CMakeFiles/mdrun.dir/md_openmm.c.o Linking CXX executable mdrun-gpu ld: warning: in /usr/local/openmm/lib/libOpenMM.dylib, file was built for i386 which is not the architecture being linked (x86_64) The above linker message clearly states what the issue is. You are compiling gromacs on and for 64 bit platform, while the OpenMM library you are trying to use is a 32 bit one. You have two options: a) either use 64 bit OpenMM or b) compile gromacs in 32 bit. AFAIR OpenMM only provides 32 bit Mac binaries so for a) you'll have to compile OpenMM in 64 bit. For b) you can add -m32 to the compiler flags and everything should work out just fine (though I have to admit that I've never tried this on a Mac). Cheers, -- Szilárd -- 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] Protein in Electric Field
Dear All I want to simulate a protein in Electric Field how can I do that? where should I start from! It's very Important for me! Please help me! Thanks -- 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] Re: still can not run md for creatine
Justin, Regarding the charges you mention, what do you think about RESP charges for this kind of compounds (drugs) parameterization? Best wishes Esteban -- On Mon, Nov 15, 2010 at 11:12 PM, Justin A. Lemkul jalem...@vt.edu wrote: Just the $0.02 that I always seem to contribute in these types of discussions - the topology you have shown below contains some likely problems. The charges (and massive charge group size) can lead to artifacts. We've got a paper due out soon about the implications of incorrect charges, but I would advise you that this topology should *not* be used for production simulation. You'd be better off spending the time to properly parameterize the molecule rather than run a bunch of simulations and get questionable (at best) or wrong (at worst) results. http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin Olga Ivchenko wrote: Hey Vitaly, Thank you for your reply. Here is the files: *itp:* ; ; ; This file was generated by PRODRG version AA081006.0504 ; PRODRG written/copyrighted by Daan van Aalten ; and Alexander Schuettelkopf ; ; Questions/comments to d...@davapc1.bioch.dundee.ac.ukmailto: d...@davapc1.bioch.dundee.ac.uk ; ; When using this software in a publication, cite: ; A. W. Schuettelkopf and D. M. F. van Aalten (2004). ; PRODRG - a tool for high-throughput crystallography ; of protein-ligand complexes. ; Acta Crystallogr. D60, 1355--1363. ; ; [ moleculetype ] Name nrexcl DRG 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OM 1 DRG OXT 1 -0.701 15.9994 2 C 1 DRG C 10.402 12.0110 3OM 1 DRG O 1 -0.701 15.9994 4 CH2 1 DRG CA 2 0.185 14.0270 5 N 1 DRG N 20.468 14.0067 6 CH3 1 DRG CAG 20.201 15.0350 7 C 1 DRG CAH 20.377 12.0110 8NZ 1 DRG NAE 2 -0.163 14.0067 9 H 1 DRG HA6 2 0.023 1.0080 10 H 1 DRG HAE 20.024 1.0080 11NZ 1 DRG NAD 2 -0.163 14.0067 12 H 1 DRG HA5 20.024 1.0080 13 H 1 DRG HAD 20.024 1.0080 [ bonds ] ; ai aj fuc0, c1, ... 2 1 20.125 1340.00.125 1340.0 ; C OXT 2 3 20.125 1340.00.125 1340.0 ; CO 2 4 2 0.153 715.00.153 715.0 ; C CA 5 4 20.147 871.00.147 871.0 ; N CA 5 6 20.147 871.00.147 871.0 ; N CAG 5 7 20.134 1050.00.134 1050.0 ; N CAH 7 8 20.134 1050.00.134 1050.0 ; CAH NAE 7 11 20.134 1050.00.134 1050.0 ; CAH NAD 8 9 20.100 1870.00.100 1870.0 ; NAE HA6 8 10 20.100 1870.00.100 1870.0 ; NAE HAE11 12 20.100 1870.00.100 1870.0 ; NAD HA511 13 20.100 1870.00.100 1870.0 ; NAD HAD [ pairs ] ; ai aj fuc0, c1, ... 1 5 1 ; OXTN 2 6 1 ; C CAG 2 7 1 ; C CAH 3 5 1 ; ON 4 8 1 ;CA NAE 4 11 1 ;CA NAD 5 9 1 ; N HA6 5 10 1 ; N HAE 5 12 1 ; N HA5 5 13 1 ; N HAD 6 8 1 ; CAG NAE 6 11 1 ; CAG NAD 8 12 1 ; NAE HA5 8 13 1 ; NAE HAD 9 11 1 ; HA6 NAD10 11 1 ; HAE NAD [ angles ] ; ai aj ak fuc0, c1, ... 1 2 3 2126.0 770.0126.0 770.0 ; OXTC O 1 2 4 2117.0 635.0117.0 635.0 ; OXTC CA 3 2 4 2117.0 635.0117.0 635.0 ; O C CA 2 4 5 2109.5 520.0109.5 520.0 ; C CAN 4 5 6 2121.0 685.0121.0 685.0 ; CAN CAG 4 5 7 2122.0 700.0122.0 700.0 ; CAN CAH 6 5 7 2117.0 635.0117.0 635.0 ; CAGN CAH 5 7 8 2120.0 670.0120.0 670.0 ; N CAH NAE 5 7 11 2120.0 670.0120.0 670.0 ; N CAH NAD 8 7 11
