[gmx-users] about box size (III)
editconf option,-f input.gro -o output.gro -bt triclinic -box 4 4 6 is not recommended for a box size of size is 3,2,6 in x,y,z use -d 0.0 instead of -box 4 4 6 Read about it here: http://www.gromacs.org/documentation/reference/online/editconf.html I am assuming that you are using periodic boundary conditions and pressure scaling. In that case -box 4 4 6 will probably be fine, but be sure to visualize your system (you could use VMD). If you are unsure about periodicity (Tsjerk recently pointed out that what looks incorrect may in fact be correct) then I urge you to turn on the periodic representation in VMD and look at the system in this manner. Chris. ___ 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] configuration of system for small molecule crystal simulations
Hi Vik, Did you make sure the (rotational) orientation of your molecule corresponded to the triclinic unit cell? And did you visualize the crystal (using e.g. genconf to extend the system)? Hope it helps, Tsjerk On 9/25/06, Vik Bajaj [EMAIL PROTECTED] wrote: Hello, I am attempting to simulate a small molecule in an orthorhombic unit cell with z=4; there is no solvent. In this case, the crystal packing forces are largely responsible for the molecular conformation, and therefore the symmetry representation is critical. I have put the molecule in a triclinic box with dimensions equal to the lattice dimensions, and I am not certain that this will result in appropriate boundary conditions. My simulation is currently blowing up, so I am revisiting the initial setup and minimization. If someone can clarify or provide an example of a similar problem, I would appreciate it very much. -Vik ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 ___ 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] g_rms, matrix and raw data
Dear all I run g_rms with -m option that produces a matrix in .xpm format. Is it possible somehow to obtain raw data i.e. the real numerical values of the elements of the matrix? Thanking in advance, Ninoo __ Yahoo! India Answers: Share what you know. Learn something new http://in.answers.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] surface tension
Dear all, what is the unit of surface tension in gromacs analysis? Is it dyn/cm or N/m. As according to me it is coming out to be in terms of N/m but it is attached with a conversion factor of some powers of 10. Kindly guide me. If I am getting e.g. 930.002 as the surface tension then what are it's units? See section 2.2 of the manual. Surface tension isn't actually defined, but after you read that, you'll know which it is. Mark ___ 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] g_rms, matrix and raw data
Dear all I run g_rms with -m option that produces a matrix in .xpm format. Is it possible somehow to obtain raw data i.e. the real numerical values of the elements of the matrix? man g_rms Mark ___ 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] surface tension
Dear all, what is the unit of surface tension in gromacs analysis? Is it dyn/cm or N/m. As according to me it is coming out to be in terms of N/m but it is attached with a conversion factor of some powers of 10. Kindly guide me. If I am getting e.g. 930.002 as the surface tension then what are it's units? regards, Pri... __ 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] water molecules in vacuum simulation.
Hi Anwar, the answer is: Yes, sure. CU Steffen Dear users, Is it possible to perform an invacuum simulation with few constrained water molecules? I dont want to use the explicit solvent, but want to use the crystallographic water molecules in protein and perform invacuum simulation. regards Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 [EMAIL PROTECTED] --- - ___ 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 -- Dipl.-Chem. Steffen Wolf Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: [EMAIL PROTECTED] Web: http://www.bph.rub.de ___ 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] surface tension
Hi Pri, Surface tension of 930.002 in gromacs units = 93.0002 mN/m or (dyn/cm) serge priyanka srivastava wrote: Dear all, what is the unit of surface tension in gromacs analysis? Is it dyn/cm or N/m. As according to me it is coming out to be in terms of N/m but it is attached with a conversion factor of some powers of 10. Kindly guide me. If I am getting e.g. 930.002 as the surface tension then what are it's units? regards, Pri... ___ 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] EM problem with OPLS and TIP4P
-Original Message- From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Wed, 20 Sep 2006 10:28 PM Subject: [gmx-users] EM problem with OPLS and TIP4P Try this: unconstrained_start = no Also ensure that your .top file is correct. Also take a look at your starting positions, where is MW? Also ensure that your waters have the correct order: eg. 871SOL OW 3496 1.935 2.093 1.901 871SOLHW1 3497 1.902 2.172 1.945 871SOLHW2 3498 1.990 2.126 1.830 871SOL MW 3499 1.938 2.107 1.898 The problema was here. In my old tip4p.itp file the water sites were in reverse order. I just change the order and it works now. Thanks. Also try outputting coords for step 20,21,22,23 in the first system and see what is actually happening. ___ 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 thewww interface or send it to [EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Check Out the new free AIM(R) Mail -- 2 GB of storage and industry-leading spam and email virus protection. ___ 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] VAL group
Title: VAL group Hello fellow gmx users, when I convert a pdb file of a peptide that contains a valyl residue into a .gro file a separate group is made for the atoms in the valyl residue. This has happened when OPLSAA/l and the GROMOS96 53a6 force fields were used. The molecule appears as one in the topology file, and the atomic description of the valyl residue in the pdb file matches that of the ffoplsa.rtp file. An excert from the topology file that shows the structure contains one peptide is below. [ system ] ; Name Protein in water [ molecules ] ; Compound #mols Protein 1 SOL 6973 An excerpt from my index file that shows the VAL group, with 16 atoms that are separated from the protein is below: 28125 28126 28127 28128 28129 28130 28131 28132 28133 28134 28135 28136 28137 28138 28139 28140 28141 28142 28143 28144 28145 28146 28147 28148 28149 28150 28151 28152 28153 28154 28155 28156 28157 28158 28159 28160 28161 28162 [ VAL ] 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 [ SOL ] 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 Could something be wrong with the pdb2gmx program? Thank you in advance for any suggestions. Sincerely, Michael Owen ___ 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] distance restraints: -merge
Title: distance restraints: -merge Fellow gmx-users, I would like to constrain the distance of an ion to specific atoms of a protein. I recently read a message in which the use of the option -merge in the pdb2gmx program was suggested. How can I use this option to form these constraints? Thank you for your assistance, Michael Owen ___ 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] Which POPC Bilayer to start?
I've had success with Tieleman's lipids. I used popc128b.pdb. Since it has the extra ns of equilibration, I figured it would cause fewer problems. However, once you start messing around with making hole in the membrane and adding a protein, you'll need to re-equilibrate again (EM PR).JimOn Sep 20, 2006, at 5:48 PM, Akshay Patny wrote:Hi AllI am trying to use POPC bilayer for doing GPCR simulation.I have come across two options of generating a POPC bilayer 1. I can generate a POPC bilayer from the VMD Membrane plug-in, wherein themembrane is generated from the pre-built membrane square patches and lipidtails are (almost) fully extended.2. Alternatively, I can download the pre-equilibrated POPC bilayer from Dr.Tieleman's website, http://moose.bio.ucalgary.ca/index.php?page=PeopleSince, I am new to the GPCR-membrane modeling, can you suggest me which outof the above two options can be a better starting point for the simulationof my GPCR protein? A membrane generated from VMD or a pre-equilibratedmembrane?? Would the equilibration time for my protein be lesser in one outof the two?If option 2 is a good idea then out of popc128a.pdb and popc128b.pdb (bothavailable from Prof. Tieleman's website), which will be a better model tostart with?Thank you very much in advance.AkshayAkshay PatnyGraduate Research AssistantFaser Hall 417, Department of Medicinal ChemistryResearch Institute of Pharmaceutical SciencesUniversity of MississippiUniversity, MS 38677E-mail: [EMAIL PROTECTED]Tel: 662-915-1286 (office); Web: www.olemiss.edu___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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 ___ 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] Problem reading large file in g_covar
Hello, I am running g_covar compiled on a sun4 architechture system running solaris 9. But the program halts with the error message that the given xtc file was not found. In fact the xtc file which is 7.1GB was very much existing. I suppose that it is a case of large file. I compiled GROMACS3.1.4 with --enable-largefile. But still the same error occurs. How to make g_covar recognise this file? ## :-) G R O M A C S (-: GRoups of Organic Molecules in ACtion for Science :-) VERSION 3.1.4 (-: Copyright (c) 1991-2002, University of Groningen, The Netherlands This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) /users/sridhar/bin/GROMACS314_SOLARIS/SERIAL/sparc-sun-solaris2.9/ultrasparc3/bin/g_covar (-: Option Filename Type Description -f50NS_WT.xtc Input Generic trajectory: xtc trr trj gro g96 pdb -s ../FILES/b4md_1cyp_WT.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb -n ../FILES/pr_1cyp_WT.ndx Input, Opt! Index file -o eigenval_WT.xvg Outputxvgr/xmgr file -v eigenvec_WT.trr OutputFull precision trajectory: trr trj -av average_WT.pdb OutputGeneric structure: gro g96 pdb -l covar_WT.log OutputLog file -xpm covar.xpm Output, Opt. X PixMap compatible matrix file -xpmacovara.xpm Output, Opt. X PixMap compatible matrix file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -niceint 0 Set the nicelevel -b time 12000 First frame (ps) to read from trajectory -e time 5 Last frame (ps) to read from trajectory -dt time -1 Only use frame when t MOD dt = first time (ps) -tu enum ps Time unit: ps, fs, ns, us, ms, s, m or h -[no]fit boolyes Fit to a reference structure -[no]ref bool no Use the deviation from the conformation in the structure file instead of from the average -[no]mwa bool no Mass-weighted covariance analysis -lastint -1 Last eigenvector to write away (-1 is till the last) Reading file ../FILES/b4md_1cyp_WT.tpr, VERSION 3.1.4 (single precision) Reading file ../FILES/b4md_1cyp_WT.tpr, VERSION 3.1.4 (single precision) Choose a group for the least squares fit Group 0 ( System) has 41820 elements Group 1 ( Protein) has 4858 elements Group 2 ( Protein-H) has 3775 elements Group 3 ( C-alpha) has 478 elements Group 4 (Backbone) has 1434 elements Group 5 ( MainChain) has 1913 elements Group 6 (MainChain+Cb) has 2361 elements Group 7 ( MainChain+H) has 2363 elements Group 8 ( SideChain) has 2495 elements Group 9 ( SideChain-H) has 1862 elements Group10 ( Prot-Masses) has 4858 elements Group11 ( Non-Protein) has 36962 elements Group12 (HEME) has47 elements Group13 ( SOL) has 36912 elements Group14 ( CL-) has 3 elements Group15 ( Other) has 36962 elements Group16 (Protein_HEME) has 4905 elements Group17 (Protein_HEME_CL-) has 4908 elements Select a group: 3 Choose a group for the covariance analysis Group 0 ( System) has 41820 elements Group 1 ( Protein) has 4858 elements Group 2 ( Protein-H) has 3775 elements Group 3 ( C-alpha) has 478 elements Group 4 (Backbone) has 1434 elements Group 5 ( MainChain) has 1913 elements Group 6 (MainChain+Cb) has 2361 elements Group 7 ( MainChain+H) has 2363 elements Group 8 ( SideChain) has 2495 elements Group 9 ( SideChain-H) has 1862 elements Group10 ( Prot-Masses) has 4858 elements Group11 ( Non-Protein) has 36962 elements Group12 (HEME) has47 elements Group13 ( SOL) has 36912 elements Group14 ( CL-) has 3 elements Group15 ( Other) has 36962 elements Group16 (Protein_HEME) has 4905 elements Group17 (Protein_HEME_CL-) has 4908 elements Select a group: 3 Note: the fit and analysis group are identical, while the fit is mass weighted and the analysis is not. Making the fit non mass weighted. Constructing covariance matrix (1434x1434)... Fatal error: File 50NS_WT.xtc not found
[gmx-users] Problem reading large file in g_covar
Hello, I am running g_covar. But the program halts with the error message that the given xtc file was not found. In fact the xtc file which is 7.1GB was very much existing. I suppose that it is a case of large file. I compiled GROMACS3.1.4 with --enable-largefile. But still the same error occurs. How to make g_covar recognise this file? ## :-) G R O M A C S (-: GRoups of Organic Molecules in ACtion for Science :-) VERSION 3.1.4 (-: Copyright (c) 1991-2002, University of Groningen, The Netherlands This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) /users/sridhar/bin/GROMACS314_SOLARIS/SERIAL/sparc-sun-solaris2.9/ultrasparc3/bin/g_covar (-: Option Filename Type Description -f50NS_WT.xtc Input Generic trajectory: xtc trr trj gro g96 pdb -s ../FILES/b4md_1cyp_WT.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb -n ../FILES/pr_1cyp_WT.ndx Input, Opt! Index file -o eigenval_WT.xvg Outputxvgr/xmgr file -v eigenvec_WT.trr OutputFull precision trajectory: trr trj -av average_WT.pdb OutputGeneric structure: gro g96 pdb -l covar_WT.log OutputLog file -xpm covar.xpm Output, Opt. X PixMap compatible matrix file -xpmacovara.xpm Output, Opt. X PixMap compatible matrix file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -niceint 0 Set the nicelevel -b time 12000 First frame (ps) to read from trajectory -e time 5 Last frame (ps) to read from trajectory -dt time -1 Only use frame when t MOD dt = first time (ps) -tu enum ps Time unit: ps, fs, ns, us, ms, s, m or h -[no]fit boolyes Fit to a reference structure -[no]ref bool no Use the deviation from the conformation in the structure file instead of from the average -[no]mwa bool no Mass-weighted covariance analysis -lastint -1 Last eigenvector to write away (-1 is till the last) Reading file ../FILES/b4md_1cyp_WT.tpr, VERSION 3.1.4 (single precision) Reading file ../FILES/b4md_1cyp_WT.tpr, VERSION 3.1.4 (single precision) Choose a group for the least squares fit Group 0 ( System) has 41820 elements Group 1 ( Protein) has 4858 elements Group 2 ( Protein-H) has 3775 elements Group 3 ( C-alpha) has 478 elements Group 4 (Backbone) has 1434 elements Group 5 ( MainChain) has 1913 elements Group 6 (MainChain+Cb) has 2361 elements Group 7 ( MainChain+H) has 2363 elements Group 8 ( SideChain) has 2495 elements Group 9 ( SideChain-H) has 1862 elements Group10 ( Prot-Masses) has 4858 elements Group11 ( Non-Protein) has 36962 elements Group12 (HEME) has47 elements Group13 ( SOL) has 36912 elements Group14 ( CL-) has 3 elements Group15 ( Other) has 36962 elements Group16 (Protein_HEME) has 4905 elements Group17 (Protein_HEME_CL-) has 4908 elements Select a group: 3 Choose a group for the covariance analysis Group 0 ( System) has 41820 elements Group 1 ( Protein) has 4858 elements Group 2 ( Protein-H) has 3775 elements Group 3 ( C-alpha) has 478 elements Group 4 (Backbone) has 1434 elements Group 5 ( MainChain) has 1913 elements Group 6 (MainChain+Cb) has 2361 elements Group 7 ( MainChain+H) has 2363 elements Group 8 ( SideChain) has 2495 elements Group 9 ( SideChain-H) has 1862 elements Group10 ( Prot-Masses) has 4858 elements Group11 ( Non-Protein) has 36962 elements Group12 (HEME) has47 elements Group13 ( SOL) has 36912 elements Group14 ( CL-) has 3 elements Group15 ( Other) has 36962 elements Group16 (Protein_HEME) has 4905 elements Group17 (Protein_HEME_CL-) has 4908 elements Select a group: 3 Note: the fit and analysis group are identical, while the fit is mass weighted and the analysis is not. Making the fit non mass weighted. Constructing covariance matrix (1434x1434)... Fatal error: File 50NS_WT.xtc not found # -- Sridhar Acharya, M Senior Research Fellow Lab
[gmx-users] Covalent bonds between topology files
Thank you for your reply, Mark. That is what I was afraid of, that I would have to physically combine the files. My only problem there is the format of the topology file that comes from pdb2gmx is slightly different than that which comes from the PRODRG server. For example, under the [ bonds ] section: (from pdb2gmx): ... 5234 52362gb_2 5237 52382gb_4 ... (and from PRODRG): ... 5252 52541 0.140 334720.0 0.140 334720.0 CAY NBN 5254 52551 0.100 374468.0 0.100 374468.0 NBN HAF ... I will try to decipher this and see what comes of it. Thankfully, the renumbering of atoms was not a problem because of the reorder.pl script available in the user contributions section. Again, thank you for your reply Mark, I hope all that I said has made sense. Cheers, W. Allen ___ 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] Regarding preparation of .itp file for a new molecule
Hai all... I am a newbie to gromacs simulation software and its file formats. I want to develop coarse grain models for surfactant systems by using atomistic simulations. I got a .pdb file for BTMAC surfactant. But to run simuations on gromacs,I need to include .itp file in source code. Can anyone of u tell me,Is it difficult to prepare a .itp file for a new molecule?? If it is so, I want to know how many days it will take to prepare... And also Please tell suggestions to prepare a .itp file for a new molecule Thanks in advance-- Arun kumar.VM.E Chemical Engg ___ 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] Covalent bonds between topology files
Hi W. Allen, This is not necessarily a problem. The gb_* labels can be found in the ffG*bon.itp files, and are replaced by the values found in those files upon preprocessing. If they both correspond to the same force field, it's no problem to combine them with some parameters referred to by codes and others written in full. You may have to worry though, regarding the force field used for both files. This should be the same for both. Best, Tsjerk On 9/26/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Thank you for your reply, Mark. That is what I was afraid of, that I would have to physically combine the files. My only problem there is the format of the topology file that comes from pdb2gmx is slightly different than that which comes from the PRODRG server. For example, under the [ bonds ] section: (from pdb2gmx): ... 5234 52362gb_2 5237 52382gb_4 ... (and from PRODRG): ... 5252 52541 0.140 334720.0 0.140 334720.0 CAY NBN 5254 52551 0.100 374468.0 0.100 374468.0 NBN HAF ... I will try to decipher this and see what comes of it. Thankfully, the renumbering of atoms was not a problem because of the reorder.pl script available in the user contributions section. Again, thank you for your reply Mark, I hope all that I said has made sense. Cheers, W. Allen ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 ___ 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] Covalent bonds between topology files
Thank you for your reply, Mark. That is what I was afraid of, that I would have to physically combine the files. My only problem there is the format of the topology file that comes from pdb2gmx is slightly different than that which comes from the PRODRG server. For example, under the [ bonds ] section: (from pdb2gmx): ... 5234 52362gb_2 5237 52382gb_4 ... (and from PRODRG): ... 5252 52541 0.140 334720.0 0.140 334720.0 CAY NBN 5254 52551 0.100 374468.0 0.100 374468.0 NBN HAF ... That's not a problem. The .itp files will have lines like #define gb_2 stuff which expands to something that resembles the latter examples, except that the bonded function number is different so the parameter lists need not match. Mark ___ 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] Regarding preparation of .itp file for a new molecule
Hai all... I am a newbie to gromacs simulation software and its file formats. I want to develop coarse grain models for surfactant systems by using atomistic simulations. I got a .pdb file for BTMAC surfactant. But to run simuations on gromacs,I need to include .itp file in source code. Can anyone of u tell me,Is it difficult to prepare a .itp file for a new molecule?? If it is so, I want to know how many days it will take to prepare... And also Please tell suggestions to prepare a .itp file for a new molecule It is tedious but not difficult to prepare an .itp file description of a molecule. Please read chapters 4 and 5 of the manual. Consider using the PRODRG server, and/or the pdb2gmx tool. Mark ___ 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] How can I remove water and ion molecules
Or you could try using the make_ndx utility, make an index file with one of the groups containing all the molecules you want to keep, then run either editconf (if want to remove them from the .gro / .pdb files) or trajconv (if want to remove them from trajectory files). Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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] Free energy calculations
Hello gmx-users,I wanted to know whether there are any tutorials available on free energy calculations with Gromacs.I have done some survey, but was curious to find out any decent tutorials available. Thanks in advance,-Vissu.-- Viswanadham Sridhara,Research Assistant,Old Dominion University,Norfolk, Va-23529. ___ 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: water molecules in vacuum simulation.
-users 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 Check Out the new free AIM(R) Mail -- 2 GB of storage and industry-leading spam and email virus protection. -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20060926/1a93ad45/attachment-0001.html -- Message: 4 Date: Tue, 26 Sep 2006 10:59:08 -0500 From: Owen, Michael [EMAIL PROTECTED] Subject: [gmx-users] VAL group To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1 Hello fellow gmx users, when I convert a pdb file of a peptide that contains a valyl residue into a .gro file a separate group is made for the atoms in the valyl residue. This has happened when OPLSAA/l and the GROMOS96 53a6 force fields were used. The molecule appears as one in the topology file, and the atomic description of the valyl residue in the pdb file matches that of the ffoplsa.rtp file. An excert from the topology file that shows the structure contains one peptide is below. [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein 1 SOL 6973 An excerpt from my index file that shows the VAL group, with 16 atoms that are separated from the protein is below: 28125 28126 28127 28128 28129 28130 28131 28132 28133 28134 28135 28136 28137 28138 28139 28140 28141 28142 28143 28144 28145 28146 28147 28148 28149 28150 28151 28152 28153 28154 28155 28156 28157 28158 28159 28160 28161 28162 [ VAL ] 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 [ SOL ] 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 Could something be wrong with the pdb2gmx program? Thank you in advance for any suggestions. Sincerely, Michael Owen -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20060926/d17613e0/attachment-0001.html -- Message: 5 Date: Tue, 26 Sep 2006 11:10:15 -0500 From: Owen, Michael [EMAIL PROTECTED] Subject: [gmx-users] distance restraints: -merge To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1 Fellow gmx-users, I would like to constrain the distance of an ion to specific atoms of a protein. I recently read a message in which the use of the option -merge in the pdb2gmx program was suggested. How can I use this option to form these constraints? Thank you for your assistance, Michael Owen -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20060926/3433c22c/attachment-0001.html -- Message: 6 Date: Tue, 26 Sep 2006 12:18:53 -0400 From: Jim Fonseca [EMAIL PROTECTED] Subject: Re: [gmx-users] Which POPC Bilayer to start? To: [EMAIL PROTECTED], Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=us-ascii I've had success with Tieleman's lipids. I used popc128b.pdb. Since it has the extra ns of equilibration, I figured it would cause fewer problems. However, once you start messing around with making hole in the membrane and adding a protein, you'll need to re-equilibrate again (EM PR). Jim On Sep 20, 2006, at 5:48 PM, Akshay Patny wrote: Hi All I am trying to use POPC bilayer for doing GPCR simulation. I have come across two options of generating a POPC bilayer 1. I can generate a POPC bilayer from the VMD Membrane plug-in, wherein the membrane is generated from the pre-built membrane square patches and lipid tails are (almost) fully extended. 2. Alternatively, I can download the pre-equilibrated POPC bilayer from Dr. Tieleman's website, http://moose.bio.ucalgary.ca/index.php?page=People Since, I am new to the GPCR-membrane modeling, can you suggest me which out of the above two options can be a better starting point for the simulation of my GPCR protein? A membrane generated from VMD or a pre- equilibrated membrane?? Would the equilibration time for my protein be lesser in one out of the two? If option 2 is a good idea then out of popc128a.pdb and popc128b.pdb (both available from Prof. Tieleman's website), which will be a better model to start with? Thank you very much in advance. Akshay Akshay Patny Graduate Research Assistant Faser Hall 417, Department of Medicinal Chemistry Research Institute of Pharmaceutical Sciences University of Mississippi University
[gmx-users] g_rotacf again
Hello everybody.I have question regarding g_rotacfIf I wanted to compute the rotational correlation function of a linear vector which is between the "centers of masses" of two groups of atoms in an individual molecule (Instead of two atoms), how do I go about it?Can I use g_rotacf to do it ?Thanks in advanceRama Talk is cheap. Use Yahoo! Messenger to make PC-to-Phone calls. Great rates starting at 1¢/min.___ 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
