Re: [gmx-users] Position restraints
On 16/06/2011 11:54 AM, Tom Dupree wrote: Greetings all, I have run into a little bit of a problem. I am trying to simulate a hetro-dimer. Through previous work we have identified 302 C-alphas (of 960 odd residues) that don't move much. Previously we position restrained these atoms in our simulations using charmm which gave us a significant speed up in simulation time. My supervisor is keen for me to do a comparison of that method with a completely unrestrained system using the 53A6 FF. I managed to generate a position restraint file using the .gro file and genrestr. However when I get to the simulation step I can't get grompp to work. As genrestr -h will warn you, its output is only useful for the first molecule. GROMACS position restraints will not give you any implementation-related speed-up, only one from reducing the sampling volume. Freeze groups will give you some speed-up (at the cost of making your results depend on your frozen configuration), but you will usually not be able to use both constraints and NPT as well. I ran genrestr -f em.gro -n subset.ndx -o subset.itp -disre -constr Such a constraint or distance restraint matrix can only work intra-[moleculetype], and so is futile for your case. As I understand my situation grompp is looking for atom numbers in subset.itp and matching them to the atom numbers in topol_Protein_chain_x.itp and since the atom numbers in subset.itp are based on the em.gro file it fails/goes out of range. Yep Thanks to some chain breaks in my structure I have 6 chains instead of 2, is there a way convert the .gro numbers into the .itp numbers? and hence generate my restraint files based on the topol_Protein_chain_x.itp files? Sure, use editconf with some appropriate index groups (and maybe -resnr) to create subset structures that will then produce output from genrestr suitable for use with grompp. Furthermore can I actually do a constraint matrix over multiple molecules? Not without uniting the [moleculetypes]. Do note that the various kinds of restraints, constraints and freeze groups are all distinct approaches, and attempting to mix them can be asking for trouble. Be sure to use the right terminology when asking for help :-) Mark Or is there a better way of achieving my desired result? (302 atoms across 2 (6) chains constrained in their relative positions) All the best, Tom Fatal error: [ file subset.itp, line 145 ]: Atom index (5222) in constraints out of bounds (1-5149). This probably means that you have inserted topology section constraints in a part belonging to a different molecule than you intended to. In that case move the constraints section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- My topology file ; ; File 'topol.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Tue May 31 11:44:23 2011 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.3 ; ; Command line was: ; pdb2gmx -f 3LP2.pdb -o 3lp2 -ignh -v ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include gromos53a6.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRES #include posre_Protein_chain_A.itp #endif #include topol_Protein_chain_A2.itp #ifdef POSRES #include posre_Protein_chain_A2.itp #endif #ifdef REST #include subset.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRES #include posre_Protein_chain_B.itp #endif #ifdef REST #include subset.itp #endif #include topol_Protein_chain_B2.itp #ifdef POSRES #include posre_Protein_chain_B2.itp #endif #ifdef REST #include subset.itp #endif #include topol_Protein_chain_B3.itp #ifdef POSRES #include posre_Protein_chain_B3.itp #endif #ifdef REST #include subset.itp #endif #include topol_Protein_chain_B4.itp #ifdef POSRES #include posre_Protein_chain_B4.itp #endif #ifdef REST #include subset.itp #endif ___ -- 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: Including quadrupole-charge interaction in GROMACS (WU Yanbin)
Hi,
Not implemented in Gromacs AFAIK.
Note that (1) even the definition of a quadruple isn't straightforwards and
depends on the orientation and (2) common FF parameters were not developed with
higher ordered multiple taken into account.
@Article{Plattner2009,
author = Plattner, N and Meuwly, M,
title = {Higher order multipole moments for molecular dynamics simulations},
journal = J Mol Model,
year = 2009,
volume = 15,
pages = 687-694
}
Ran
Ran Friedman
Biträdande Lektor (Assistant Professor)
Linnaeus University
School of Natural Sciences
391 82 Kalmar, Sweden
Norrgård, room 328d
+46 480 446 290 Telephone
+46 76 207 8763 Mobile
ran.fried...@lnu.se
http://lnu.se/ccbg
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of gmx-users-requ...@gromacs.org [gmx-users-requ...@gromacs.org]
Sent: 16 June 2011 09:00
To: gmx-users@gromacs.org
Subject: gmx-users Digest, Vol 86, Issue 96
Send gmx-users mailing list submissions to
gmx-users@gromacs.org
To subscribe or unsubscribe via the World Wide Web, visit
http://lists.gromacs.org/mailman/listinfo/gmx-users
or, via email, send a message with subject or body 'help' to
gmx-users-requ...@gromacs.org
You can reach the person managing the list at
gmx-users-ow...@gromacs.org
When replying, please edit your Subject line so it is more specific
than Re: Contents of gmx-users digest...
Today's Topics:
1. Re: CHARMM forcefield (Justin A. Lemkul)
2. Re: local pressure calcuation for Gromacs-4.5 (Justin A. Lemkul)
3. Including quadrupole-charge interaction in GROMACS (WU Yanbin)
4. g_density (chris.ne...@utoronto.ca)
5. Position restraints (Tom Dupree)
6. Re: Position restraints (Mark Abraham)
--
Message: 1
Date: Wed, 15 Jun 2011 17:11:08 -0400
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] CHARMM forcefield
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4df91fec.8080...@vt.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
simon sham wrote:
Hi,
I have two questions about using the charmm force field.
1. Do we still need to use the two perl scripts, convert_charmm_
to_gromacs.pl and fix_top_for_charmm.pl?
No.
2. I got the following note when I tried to do energy minim. with grompp:
NOTE 1 [file topol.top]:
The largest charge group contains 12 atoms.
Since atoms only see each other when the centers of geometry of the charge
groups they belong to are within the cut-off distance, too large charge
groups can lead to serious cut-off artifacts.
For efficiency and accuracy, charge group should consist of a few atoms.
For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
Is this a problem?
Yes. CHARMM topologies should not use charge groups. You should invoke pdb2gmx
with the -nochargegrp option to create a proper topology.
-Justin
Thanks for your insight!
Simon
--
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
--
Message: 2
Date: Wed, 15 Jun 2011 17:17:53 -0400
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] local pressure calcuation for Gromacs-4.5
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4df92181.2090...@vt.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Amit Choubey wrote:
Dear all,
Could anyone direct me to the manual for local pressure calculation or a
place where everything is mentioned about it ? I have been only able to
collect bits and pieces from the mailing lists.
That's probably all there is to be found. There's no manual linked from the git
web interface or the ftp site.
-Justin
Thank you
Amit
On Wed, Jun 15, 2011 at 5:35 AM, Mark Abraham mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au wrote:
On 15/06/2011 9:09 PM, Jianguo Li wrote:
Dear all,
I have made a test calculation of local pressure using version 4.5
for my membrane simulation using CHARMM FF. When rerun the
simulation, mdrun gives the localpressure data. Howeve, instead of
giving an anveraged data of the local pressure, mdrun gives a
separate file for each frame, so I got many files:
localpressure.dat0, localpressure.dat1, localpressure.dat2,
localpressure.dat3 ..
Then I need to calculate the pressure tensor for each frame and
make average. but these localpressure.dat files are very big (each
file is about 30 Mb), occupying large space of the hard disk. Can
[gmx-users] Implicit solvent calculatiom
Hi, My system is protein +DNA. I am trying to perform implicit solvent calculation using Amber 99. In the begging I wanted to minimize the system and got this error message. GB parameter(s) missing or negative for atom type 'OS' GB parameter(s) missing or negative for atom type 'H2' GB parameter(s) missing or negative for atom type 'N*' GB parameter(s) missing or negative for atom type 'CM' GB parameter(s) missing or negative for atom type 'P' --- Program grompp, VERSION 4.5.4 Source code file: grompp.c, line: 1123 Fatal error: Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for 5 atomtypes or they might be negative. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors All the atoms, in which parametres are missing belong to DNA. Should I add them manually to gbsa.itp? ( but i don't know the right parameters?). Thanks in advance. Netaly Khazanov. Post-doctoral student. -- 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] Position restraints with multiple identical molecules
Dear All, My system consists of 32 identical molecules (with 91 atoms per molecule). I would like to apply a position restraint to the 91st atom of each molecules. Since all my molecules are identical I only have one [moleculetype] which contains 91 atoms. I have defined -DPOSRES in the .mdp file and have placed: #ifdef POSRES #include posre.itp #endif in (hopefully) the correct part of the topology file (immediately below the only [moleculetype]). There are no solvent molecules or ions. Applying a position restraint to atom 91 works fine with posre.itp containing: [ position_restraints ] ; ai funct fc (in x, y and z) 91 1 2000 2000 2000 This results in just one restraint to atom 91. But if I want to restrain the 91st atom in the second molecule (atom 182 in the .gro file), how do I do it? [ position_restraints ] ; ai funct fc (in x, y and z) 91 1 2000 2000 2000 182 1 2000 2000 2000 Does not work since 182 is outside the atom numbers in the [moleculetype] (1 to 91). Similarly, having 32 lines in posre.itp reading 91 1 2000 2000 2000 gives 32 position restraints to atom 91. I expect I can get around this problem by duplicating the current topology 32 times and creating a huge topol.top file with all 2912 atoms defined explicitly. However, it seems there should be a more elegant way to achieve this. Any help would be greatly appreciated! I have included below a simplified example with all the other atoms removed. In this case, how do you restrain the position of atom 2,3,4 and 5? Craig Craig Kitchen Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK topol.top: [ moleculetype ] ; Atom ; Name nrexcl UNK3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 amber99_41 1 UNK OAI 1 -0.50762 15.9994 ; Include Position restraint file #ifdef POSRES #include posre.itp #endif [ system ] ; Name Multiple Atoms [ molecules ] ; Compound#mols UNK 5 Starting conf.gro: Multiple Atoms 5 1UNKOAI1 0.767 1.527 0.970 2UNKOAI2 0.988 0.716 1.774 3UNKOAI3 0.556 0.587 0.434 4UNKOAI4 0.335 1.656 2.436 5UNKOAI5 0.766 1.527 2.373 2.64620 3.76260 2.80720 File used for restraint coordinates (grompp -r) : Restraint coordinates 5 1UNKOAI1 0.000 1.500 1.000 2UNKOAI2 1.100 0.621 2.000 3UNKOAI3 0.399 0.621 0.349 4UNKOAI4 0.221 1.562 -0.343 5UNKOAI5 0.923 1.561 2.458 2.64620 3.76260 2.80720 -- 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] Position restraints with multiple identical molecules
Craig Kitchen wrote: Dear All, My system consists of 32 identical molecules (with 91 atoms per molecule). I would like to apply a position restraint to the 91st atom of each molecules. Since all my molecules are identical I only have one [moleculetype] which contains 91 atoms. I have defined -DPOSRES in the .mdp file and have placed: #ifdef POSRES #include posre.itp #endif in (hopefully) the correct part of the topology file (immediately below the only [moleculetype]). There are no solvent molecules or ions. Applying a position restraint to atom 91 works fine with posre.itp containing: [ position_restraints ] ; ai funct fc (in x, y and z) 91 1 2000 2000 2000 This results in just one restraint to atom 91. But if I want to restrain the 91st atom in the second molecule (atom 182 in the .gro file), how do I do it? You already are. The [position_restraints] directive is applied to the atom(s) of the [moleculetype] that contains it, so if you only have one [moleculetype] then any instance of it will have the restraint applied to whatever atoms are indicated. -Justin [ position_restraints ] ; ai funct fc (in x, y and z) 91 1 2000 2000 2000 182 1 2000 2000 2000 Does not work since 182 is outside the atom numbers in the [moleculetype] (1 to 91). Similarly, having 32 lines in posre.itp reading 91 1 2000 2000 2000 gives 32 position restraints to atom 91. I expect I can get around this problem by duplicating the current topology 32 times and creating a huge topol.top file with all 2912 atoms defined explicitly. However, it seems there should be a more elegant way to achieve this. Any help would be greatly appreciated! I have included below a simplified example with all the other atoms removed. In this case, how do you restrain the position of atom 2,3,4 and 5? Craig Craig Kitchen Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK topol.top: [ moleculetype ] ; Atom ; Name nrexcl UNK3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 amber99_41 1 UNK OAI 1 -0.50762 15.9994 ; Include Position restraint file #ifdef POSRES #include posre.itp #endif [ system ] ; Name Multiple Atoms [ molecules ] ; Compound#mols UNK 5 Starting conf.gro: Multiple Atoms 5 1UNKOAI1 0.767 1.527 0.970 2UNKOAI2 0.988 0.716 1.774 3UNKOAI3 0.556 0.587 0.434 4UNKOAI4 0.335 1.656 2.436 5UNKOAI5 0.766 1.527 2.373 2.64620 3.76260 2.80720 File used for restraint coordinates (grompp -r) : Restraint coordinates 5 1UNKOAI1 0.000 1.500 1.000 2UNKOAI2 1.100 0.621 2.000 3UNKOAI3 0.399 0.621 0.349 4UNKOAI4 0.221 1.562 -0.343 5UNKOAI5 0.923 1.561 2.458 2.64620 3.76260 2.80720 -- 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
[gmx-users] Re: gmx-users Digest, Vol 86, Issue 97
Dear Sir, I found an error which is given below as i run grompp for position-restraint Fatal error: Group DRG not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. The error was attempted with -n but the following error also found, File input/output error: index.ndx I can do nothing by this simple statement, please help me, Sir Regards with, Ithayaraja M.. -- 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] Group DRG not found in indexfile
Please choose an informative subject line, especially when initiating a new thread. ITHAYARAJA wrote: Dear Sir, I found an error which is given below as i run grompp for position-restraint Fatal error: Group DRG not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. The error was attempted with -n but the following error also found, File input/output error: index.ndx I can do nothing by this simple statement, please help me, Sir You've specified a group somewhere in the .mdp that doesn't exist. Groups can be assigned by the name given in the [moleculetype] directive or by a custom name given in an index file. Apparently you've invoked grompp -n but you don't have an index file. You may or may not need one. If you've used DRG but no [moleculetype] entries are named as such, use a proper name. If you need to use some custom subset of atoms, make an index group. -Justin -- 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] Position restraints with multiple identical molecules
You already are. The [position_restraints] directive is applied to the atom(s) of the [moleculetype] that contains it, so if you only have one [moleculetype] then any instance of it will have the restraint applied to whatever atoms are indicated. -Justin Hi Justin, thanks for your reply. If this is the case then should I not expect to see all the position restraints in the .tpr file? Using gmxdump -s md1.tpr to inspect the file I can only see Position Rest.: nr: 2 iatoms: 0 type=1 (POSRES) 0 (this is on the simplified 5 atom case). Which implies there is one position restraint on atom 1 (index 0 I guess). Craig Craig Kitchen wrote: Dear All, My system consists of 32 identical molecules (with 91 atoms per molecule). I would like to apply a position restraint to the 91st atom of each molecules. Since all my molecules are identical I only have one [moleculetype] which contains 91 atoms. I have defined -DPOSRES in the .mdp file and have placed: #ifdef POSRES #include posre.itp #endif in (hopefully) the correct part of the topology file (immediately below the only [moleculetype]). There are no solvent molecules or ions. Applying a position restraint to atom 91 works fine with posre.itp containing: [ position_restraints ] ; ai funct fc (in x, y and z) 91 1 2000 2000 2000 This results in just one restraint to atom 91. But if I want to restrain the 91st atom in the second molecule (atom 182 in the .gro file), how do I do it? You already are. The [position_restraints] directive is applied to the atom(s) of the [moleculetype] that contains it, so if you only have one [moleculetype] then any instance of it will have the restraint applied to whatever atoms are indicated. -Justin [ position_restraints ] ; ai funct fc (in x, y and z) 91 1 2000 2000 2000 182 1 2000 2000 2000 Does not work since 182 is outside the atom numbers in the [moleculetype] (1 to 91). Similarly, having 32 lines in posre.itp reading 91 1 2000 2000 2000 gives 32 position restraints to atom 91. I expect I can get around this problem by duplicating the current topology 32 times and creating a huge topol.top file with all 2912 atoms defined explicitly. However, it seems there should be a more elegant way to achieve this. Any help would be greatly appreciated! I have included below a simplified example with all the other atoms removed. In this case, how do you restrain the position of atom 2,3,4 and 5? Craig Craig Kitchen Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK topol.top: [ moleculetype ] ; Atom ; Name nrexcl UNK 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 amber99_41 1 UNK OAI 1 -0.50762 15.9994 ; Include Position restraint file #ifdef POSRES #include posre.itp #endif [ system ] ; Name Multiple Atoms [ molecules ] ; Compound#mols UNK 5 Starting conf.gro: Multiple Atoms 5 1UNKOAI1 0.767 1.527 0.970 2UNKOAI2 0.988 0.716 1.774 3UNKOAI3 0.556 0.587 0.434 4UNKOAI4 0.335 1.656 2.436 5UNKOAI5 0.766 1.527 2.373 2.64620 3.76260 2.80720 File used for restraint coordinates (grompp -r) : Restraint coordinates 5 1UNKOAI1 0.000 1.500 1.000 2UNKOAI2 1.100 0.621 2.000 3UNKOAI3 0.399 0.621 0.349 4UNKOAI4 0.221 1.562 -0.343 5UNKOAI5 0.923 1.561 2.458 2.64620 3.76260 2.80720 -- 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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] an error for .tpr files
Hi all I want to run a program in a Quad Core PC and in cluster. the program was run succesfuly in my PC but when I run it in cluster I have the following error. Would you please help me? Can not open file: topol.tpr the .tpr file filename.tpr that I want run it is in my folder. Thanks alot Regards Elena -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] residue HISB not found 4.5.3 versus 4.0.7 OPLSAA
Hi I had a simulation run with 4.0.7, using opls-aa for a protein in water. I now use part of the protein coordinates output from the simulation, and use pdb2gmx as: pdb2gmx -f conf.gro -ff oplsaa -ignh pdb2gmx complains that it cannot find HISB. I checked that the topology files in 4.5.3 do not contain HISB, while those in 4.0.7 do. It does not suffice to create another copy of the HISE topology in the .rtp file and call it HISB, because a number of hydrogen atoms also have been renamed? What can be done? I want to use 4.5.3 because I would prefer to retain residue numbering Maria -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Position restraints with multiple identical molecules
Hi Justin, Ok - the .tpr file only lists the atoms from the molecule type. I get it now. Thanks again! Craig On 16 Jun 2011, at 12:58, Justin A. Lemkul wrote: Craig Kitchen wrote: Dear All, My system consists of 32 identical molecules (with 91 atoms per molecule). I would like to apply a position restraint to the 91st atom of each molecules. Since all my molecules are identical I only have one [moleculetype] which contains 91 atoms. I have defined -DPOSRES in the .mdp file and have placed: #ifdef POSRES #include posre.itp #endif in (hopefully) the correct part of the topology file (immediately below the only [moleculetype]). There are no solvent molecules or ions. Applying a position restraint to atom 91 works fine with posre.itp containing: [ position_restraints ] ; ai funct fc (in x, y and z) 91 1 2000 2000 2000 This results in just one restraint to atom 91. But if I want to restrain the 91st atom in the second molecule (atom 182 in the .gro file), how do I do it? You already are. The [position_restraints] directive is applied to the atom(s) of the [moleculetype] that contains it, so if you only have one [moleculetype] then any instance of it will have the restraint applied to whatever atoms are indicated. -Justin [ position_restraints ] ; ai funct fc (in x, y and z) 91 1 2000 2000 2000 182 1 2000 2000 2000 Does not work since 182 is outside the atom numbers in the [moleculetype] (1 to 91). Similarly, having 32 lines in posre.itp reading 91 1 2000 2000 2000 gives 32 position restraints to atom 91. I expect I can get around this problem by duplicating the current topology 32 times and creating a huge topol.top file with all 2912 atoms defined explicitly. However, it seems there should be a more elegant way to achieve this. Any help would be greatly appreciated! I have included below a simplified example with all the other atoms removed. In this case, how do you restrain the position of atom 2,3,4 and 5? Craig Craig Kitchen Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK topol.top: [ moleculetype ] ; Atom ; Name nrexcl UNK 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 amber99_41 1 UNK OAI 1 -0.50762 15.9994 ; Include Position restraint file #ifdef POSRES #include posre.itp #endif [ system ] ; Name Multiple Atoms [ molecules ] ; Compound#mols UNK 5 Starting conf.gro: Multiple Atoms 5 1UNKOAI1 0.767 1.527 0.970 2UNKOAI2 0.988 0.716 1.774 3UNKOAI3 0.556 0.587 0.434 4UNKOAI4 0.335 1.656 2.436 5UNKOAI5 0.766 1.527 2.373 2.64620 3.76260 2.80720 File used for restraint coordinates (grompp -r) : Restraint coordinates 5 1UNKOAI1 0.000 1.500 1.000 2UNKOAI2 1.100 0.621 2.000 3UNKOAI3 0.399 0.621 0.349 4UNKOAI4 0.221 1.562 -0.343 5UNKOAI5 0.923 1.561 2.458 2.64620 3.76260 2.80720 -- 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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] residue HISB not found 4.5.3 versus 4.0.7 OPLSAA
On 16/06/2011 11:01 PM, maria goranovic wrote: Hi I had a simulation run with 4.0.7, using opls-aa for a protein in water. I now use part of the protein coordinates output from the simulation, and use pdb2gmx as: pdb2gmx -f conf.gro -ff oplsaa -ignh pdb2gmx complains that it cannot find HISB. I checked that the topology files in 4.5.3 do not contain HISB, while those in 4.0.7 do. It does not suffice to create another copy of the HISE topology in the .rtp file and call it HISB, because a number of hydrogen atoms also have been renamed? What can be done? I want to use 4.5.3 because I would prefer to retain residue numbering Rename all the HISB residues in your input coordinate file to whatever OPLS/AA wants. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] an error for .tpr files
On 16/06/2011 10:35 PM, Maria Hamilton wrote: Hi all I want to run a program in a Quad Core PC and in cluster. the program was run succesfuly in my PC but when I run it in cluster I have the following error. Would you please help me? Can not open file: topol.tpr the .tpr file filename.tpr that I want run it is in my folder. You're doing it wrong, but you haven't told us how you're doing anything. This error means you haven't specified -s filename.tpr, one way or another. 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] residue HISB not found 4.5.3 versus 4.0.7 OPLSAA
thought of that, but the trajectory also has HISB data .. so I guess I will have to alter it frame by frame ? On Thu, Jun 16, 2011 at 4:32 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 16/06/2011 11:01 PM, maria goranovic wrote: Hi I had a simulation run with 4.0.7, using opls-aa for a protein in water. I now use part of the protein coordinates output from the simulation, and use pdb2gmx as: pdb2gmx -f conf.gro -ff oplsaa -ignh pdb2gmx complains that it cannot find HISB. I checked that the topology files in 4.5.3 do not contain HISB, while those in 4.0.7 do. It does not suffice to create another copy of the HISE topology in the .rtp file and call it HISB, because a number of hydrogen atoms also have been renamed? What can be done? I want to use 4.5.3 because I would prefer to retain residue numbering Rename all the HISB residues in your input coordinate file to whatever OPLS/AA wants. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] residue HISB not found 4.5.3 versus 4.0.7 OPLSAA
On 17/06/2011 12:33 AM, maria goranovic wrote: thought of that, but the trajectory also has HISB data .. .xtc and .trr trajectories have no atom identification. That's why lots of the tools require a .tpr or coordinate file, together with a trajectory file in order to function. Using bash, look at gmxdump -f traj.xtc 21|less to learn what is there. You merely need to be confident the atom ordering hasn't changed from whatever generated the old trajectory. so I guess I will have to alter it frame by frame ? Even if your trajectory is some pseudo-format like .pdb or .gro, you can convert it back to one of the above easily. Mark On Thu, Jun 16, 2011 at 4:32 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 16/06/2011 11:01 PM, maria goranovic wrote: Hi I had a simulation run with 4.0.7, using opls-aa for a protein in water. I now use part of the protein coordinates output from the simulation, and use pdb2gmx as: pdb2gmx -f conf.gro -ff oplsaa -ignh pdb2gmx complains that it cannot find HISB. I checked that the topology files in 4.5.3 do not contain HISB, while those in 4.0.7 do. It does not suffice to create another copy of the HISE topology in the .rtp file and call it HISB, because a number of hydrogen atoms also have been renamed? What can be done? I want to use 4.5.3 because I would prefer to retain residue numbering Rename all the HISB residues in your input coordinate file to whatever OPLS/AA wants. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Including quadrupole-charge interaction in GROMACS
Hi, Erik, Thanks for the information. Regarding using more than two partial charges to mimic quadrupole explicitly, is there a one-to-one relation between the quadrupole moments and position and magnitude of the partial charges? For example, if I would like to include quadrupole moment for carbon in graphene, which has only non-zero Q20 quadrupole component, how should I place partial charges to mimic that quadrupole moment? Any hint or direction for literature is appreciated. Best, Yanbin On Thu, Jun 16, 2011 at 3:24 AM, Erik Marklund er...@xray.bmc.uu.se wrote: Quadrupole interactions are implicit whenever you have a molecule withe more than two partial charges. You don't have to include it explicitly. There are, however, multipole expansion techniques to speed up electrostatics calculations, but that's another story. Erik 15 jun 2011 kl. 23.45 skrev WU Yanbin: Dear GMXers, Is there a way in GROMACS to include quadrupole-charge interaction? Or is there a standard to way to mimic quadrupole moment using partial charge? Thank you. Best, Yanbin -- 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 --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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_dist
Hello, I have a system with 128 emi (cations) and 128 Cl (anions). I want to calculate how many CL atoms are in cutoff distance relative to hydorgen aotm of cation. I considered all CL atoms are distinguishable. Basically I want to calcualte the distance between each CL atom and correponing hydorgen and registered those CL atoms which are whthin cutoff. How can I do ? I am using Gromacs 4.0.7 version. Thanks Nilesh -- 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] Including quadrupole-charge interaction in GROMACS
Hi, For neutral species, I think it's straightforward (unless the paper Ran Friedman mentioned says otherwise). Just use the definition of the quadrupole moment to figure out where to put the charges and what magnitude to assign to them. The electric field from a quadrupole declines like r^-3, however, so its importance for graphene interactions seem very small to me. Erik 16 jun 2011 kl. 17.10 skrev WU Yanbin: Hi, Erik, Thanks for the information. Regarding using more than two partial charges to mimic quadrupole explicitly, is there a one-to-one relation between the quadrupole moments and position and magnitude of the partial charges? For example, if I would like to include quadrupole moment for carbon in graphene, which has only non-zero Q20 quadrupole component, how should I place partial charges to mimic that quadrupole moment? Any hint or direction for literature is appreciated. Best, Yanbin On Thu, Jun 16, 2011 at 3:24 AM, Erik Marklund er...@xray.bmc.uu.se wrote: Quadrupole interactions are implicit whenever you have a molecule withe more than two partial charges. You don't have to include it explicitly. There are, however, multipole expansion techniques to speed up electrostatics calculations, but that's another story. Erik 15 jun 2011 kl. 23.45 skrev WU Yanbin: Dear GMXers, Is there a way in GROMACS to include quadrupole-charge interaction? Or is there a standard to way to mimic quadrupole moment using partial charge? Thank you. Best, Yanbin -- 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 --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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 --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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_hbond
Hi, I am little confused about setting up the two groups in g_hbond. 1. Are the two groups corresponding to the donor (N) and the acceptor (O) atoms? I want to measure the lifetime, angle and distance of the triplet N-HO hydrogen bond. Is this the triplet that the manual talks about? Thanks for your insight. Simon -- 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_dist
Dear Nilesh: You don't seem to have made any progress since Mark gave you some reading hints. Your best chance to get a useful response follows the general form: 1. I want to do A. 2. I tried method B, here are the exact commands that I used (copy and paste) 3. With that method, I obtain C 4. But I am confused about why C does not look like D. 5. What is the problem? Basically, it helps to show that you are doing your own work too. For example, try a command on a single frame and then look at that frame with VMD and count for yourself and verify the answer that way. Chris. -- original message -- I have a system with 128 emi (cations) and 128 Cl (anions). I want to calculate how many CL atoms are in cutoff distance relative to hydorgen aotm of cation. I considered all CL atoms are distinguishable. Basically I want to calcualte the distance between each CL atom and correponing hydorgen and registered those CL atoms which are whthin cutoff. How can I do ? I am using Gromacs 4.0.7 version. Thanks Nilesh -- 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] Can't unfold the protein
Hi, I have question about unfolding. I use three different ways respectively but all failed. The three way is, 1. 600K in 20ns, then the system explode. 2. 400K in 10ns, the protein is very stable and the value is almost the same in radius of gyration. 3. heating up from 300K to 400K in 2ns and the other 2ns for 400K only, then the protein is still stable and the value is almost the same in radius of gyration. Below is the mdp file of the heating. What's wrong with my system? regards, Hsin-Lin - title#160;#160;#160;#160;#160;#160;#160; = ttt cpp#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; /lib/cpp constraints#160;#160;#160;#160;#160;#160;#160;#160; =#160; hbonds ;define#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; -DFLEX_SPC integrator#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; md emtol#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 100.0 emstep#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 0.005 dt#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 0.002#160;#160;#160; ; ps ! nsteps#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 200#160; ; total 4 ns nstcomm#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 500 nstxout#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 500 nstvout#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 500 nstfout#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 500 nstlog#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 500 nstenergy#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 500 nstlist#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 5 ns_type#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; grid rlist#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 1. rcoulomb#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 1. rvdw#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 1. coulombtype#160;#160;#160;#160;#160;#160;#160;#160; =#160; PME fourierspacing#160;#160;#160;#160;#160; =#160; 0.12 pme_order#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 4 optimize_fft#160;#160;#160;#160;#160;#160;#160; =#160; yes Tcoupl#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; v-rescale tc-grps#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; Protein Non-Protein ;tau_t#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 0.1#160; 0.1 tau_t#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 0.2 0.2 ref_t#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 300 300 energygrps#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; A-chain B-chain SOL#160; NA+ Pcoupl#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; berendsen Pcoupltype#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; isotropic ;tau_p#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 0.1 tau_p#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 0.25 compressibility#160;#160;#160;#160; =#160; 5.4e-5 ref_p#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 1.0 gen_vel#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; yes gen_temp#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 300 gen_seed#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 173529 ; Annealing annealing#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; single single annealing_npoints#160;#160; =#160; 21 21 annealing_time#160;#160;#160;#160;#160; =#160; 0 100 200 300 400 500 600 700 800 900 1000 1100 1200 1300 1400 1500 1600 1700 1800 1900 2000 0 100 200 300 400 500 600 700 800 900 1000 1100 1200 1300 1400 1500 1600 1700 1800 1900 2000 annealing_temp#160;#160;#160;#160;#160; =#160; 300 305 310 315 320 325 330 335 340 345 350 355 360 365 370 375 380 385 390 395 400 300 305 310 315 320 325 330 335 340 345 350 355 360 365 370 375 380 385 390 395 400 - -- 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] Can't unfold the protein
Dear Hsin-Lin: The first thing that comes to mind is using very high temperatures with NVT. Obtaining the desired denatured state is a complex challenge, but you might try this paper: Phys. Rev. Lett. 93, 238105 (2004) Reversible Temperature and Pressure Denaturation of a Protein Fragment: A Replica Exchange Molecular Dynamics Simulation Study Still, your post seems to be about simply being unable to unfold at all. I have unfolded a very stable beta-barrel by either simulating at 3000 K or using the pull code to pull the termini apart. This was not a real study -- I only used this to make a reverse folding movie for non-scientists -- but I can verify that it is possible to unfold even very stable proteins by these methods. Chris. -- original message -- Hi, I have question about unfolding. I use three different ways respectively but all failed. The three way is, 1. 600K in 20ns, then the system explode. 2. 400K in 10ns, the protein is very stable and the value is almost the same in radius of gyration. 3. heating up from 300K to 400K in 2ns and the other 2ns for 400K only, then the protein is still stable and the value is almost the same in radius of gyration. Below is the mdp file of the heating. What's wrong with my system? -- 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] Implicit solvent calculatiom
On 16/06/2011 7:59 PM, Netaly Khazanov wrote: Hi, My system is protein +DNA. I am trying to perform implicit solvent calculation using Amber 99. In the begging I wanted to minimize the system and got this error message. GB parameter(s) missing or negative for atom type 'OS' GB parameter(s) missing or negative for atom type 'H2' GB parameter(s) missing or negative for atom type 'N*' GB parameter(s) missing or negative for atom type 'CM' GB parameter(s) missing or negative for atom type 'P' --- Program grompp, VERSION 4.5.4 Source code file: grompp.c, line: 1123 Fatal error: Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for 5 atomtypes or they might be negative. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors All the atoms, in which parametres are missing belong to DNA. Should I add them manually to gbsa.itp? ( but i don't know the right parameters?). I expect you're going to have to check in the literature whether such parameters exist. Unfortunately, not every combination of everything can be available in a nice shrink-wrapped package :) Once you've found them, then you'll have to fill in the columns of the above-mentioned section accordingly. 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
[gmx-users] Can't unfold the protein
Dear Chris, Thank you for your reply. My protein is very stable. I simulated it in 300ns in 300K before but there was almost no change. That's why I want to do denaturation now. I want to start a new simulation on the protein which is unfolded. And I'll read the paper you told me. Thank you. But I don't understand what you recommend me to do. You use 3000K on your protein and the protein unfolded. I use 600K on my protein but the system explode(box become very big and protein locate at corner). I saw the second way on this web, http://manual.gromacs.org/online/protunf.html But it also useless to me. And in my mdp I use thermostat and barostat, which means my system is NPT. Does anything wrong in my methods? Sincerely yours, Hsin-Lin -- 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] Gromacs to Amber trajectory
Dear All, I have created Amber input file (.prmtop and .rst7) using Xleap. And then I have converted this input file into Gromacs input file format (*.gro and *.top) with amb2gmx.pl script. I did simulation using Gromacs Package (Amber Force Field). Now I would like to convert Gromacs trajectory file to Amber trajectory file format. So that I can easily analyses this trajectory. I tried to convert Gromacs trajectory file to Amber trajectory file using VMD. This VMD converted trajectory is not working fine. Pls help me in this regards Eagerly waiting for your suggestion. Regards Raja -- 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] Can't unfold the protein
Dear Hsin-Lin: I am no expert in this area. I am just saying that if you get densities that are way too low in NPT, then you might alleviate this problem with NVT. In fact, I would personally do this in vacuum without pbc and use the sd integrator. Then you can sample extended conformations. I'd consider this a method to generate unfolded conformations that probably have no relation to the true temperature denatured state. But let's be honest, you're never going to come close to Boltzmann sampling of an unfolded state in 300 ns so why bother with the water? Your link ( http://manual.gromacs.org/online/protunf.html ) is only concerned with analysis, so it is irrelevant. If you are determined to use NPT then I suppose that you could use the Berendsen barostat (more stable in simulations but you get the wrong ensemble) with a very low compressibility. That's about all I can say, perhaps somebody else will comment. Good luck, Chris. -- original message -- Dear Chris, Thank you for your reply. My protein is very stable. I simulated it in 300ns in 300K before but there was almost no change. That's why I want to do denaturation now. I want to start a new simulation on the protein which is unfolded. And I'll read the paper you told me. Thank you. But I don't understand what you recommend me to do. You use 3000K on your protein and the protein unfolded. I use 600K on my protein but the system explode(box become very big and protein locate at corner). I saw the second way on this web, http://manual.gromacs.org/online/protunf.html But it also useless to me. And in my mdp I use thermostat and barostat, which means my system is NPT. Does anything wrong in my methods? Sincerely yours, Hsin-Lin -- 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] gmx4.5.4 genion problem: No line with moleculetype 'SOL' found
Hi, everyone: I am a new user of Gromacs, and I am running through the tutorial. When I am trying to run the ligand-receptor binding tutorial from http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html I met some trouble in adding ion. Each time when I use genion, it shows: Will try to add 0 NA ions and 6 CL ions. Select a continuous group of solvent molecules Group 0 ( System) has 33046 elements Group 1 (Protein) has 1693 elements Group 2 ( Protein-H) has 1301 elements Group 3 (C-alpha) has 163 elements Group 4 ( Backbone) has 489 elements Group 5 ( MainChain) has 653 elements Group 6 ( MainChain+Cb) has 805 elements Group 7 (MainChain+H) has 815 elements Group 8 ( SideChain) has 878 elements Group 9 (SideChain-H) has 648 elements Group10 (Prot-Masses) has 1693 elements Group11 (non-Protein) has 31353 elements Group12 ( Other) has15 elements Group13 (JZ4) has15 elements Group14 ( Water) has 31338 elements Group15 (SOL) has 31338 elements Group16 ( non-Water) has 1708 elements Select a group: 15 Selected 15: 'SOL' Number of (3-atomic) solvent molecules: 10446 Processing topology Back Off! I just backed up temp.top to ./#temp.top.3# --- Program genion_d, VERSION 4.5.4 Source code file: gmx_genion.c, line: 285 Fatal error: No line with moleculetype 'SOL' found the [ molecules ] section of file 'topol.top' I checked my topology file and it looks fine: ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include gromos43a1.ff/spc.itp ; Include ligand topoloty #include drg.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include gromos43a1.ff/ions.itp [ system ] ; Name Protein [ molecules ] ; Compound#mols Protein_chain_A 1 JZ4 1 SOL 10446 One thing that might happen is in the genion source file, I read through it, and the problem either happens in loading the line to buf2, or in the gmx_strcmp(buf2,SOL), since clearly the SOL_line is -1 aftermath. The other thing I tried is to remove the ligand JZ4 part in both topology and coordinates file, and in this case, it works perfectly for adding ion. But in this way, I do not know how to insert my ligand into the system since it might collide with solvent. Can someone help me with this problem? Thank you all very much. Ye Yang -- 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] Can't unfold the protein
Hey, NPT is not the appropriate way to do this kind of simulations. I am not sure whether or not the water models available for classic MD simulations are able to reproduce the phase behavior. Indeed what you see when your system explodes and gets huge is the water evaporating. What is generally done is to allow the system to reach the density of liquid water at the temperature that you desire (see the Dagget's papers of that) and then use NVT for the rest of the simulation. Regarding the kinetics of the process it is up to the protein. There are some proteins that unfold really fast and others reallly really slow. For instance, on one of my systems i have to simulate 50 ns at 600 K to only see a 40% decrease in structure. As you may already imagine, the pressure gets quite high in these kind of simulations. Extreme pressure can also induce protein unfolding, but the depence here is again protein dependent since moderately high pressure tends to stabilize the structure. Of course what is moderate and what is high is case dependent. Please consider also that biomolecular forcefields were not designed with these extreme temperatures in mind, so while doing high temperature induced unfolding you are taking the FF to the limit and you should be extremely careful of what kind of conclusion you obtain from your simulation. Regards Felipe Mensaje originalDe: chris.neale@utoronto.caFecha: 16-jun-2011 12:58Para: gmx-users@gromacs.orgAsunto: [gmx-users] Canamp;#39;t unfold the proteinDear Hsin-Lin:I am no expert in this area. I am just saying that if you get densities that are way too low in NPT, then you might alleviate this problem with NVT.In fact, I would personally do this in vacuum without pbc and use the sd integrator. Then you can sample extended conformations. I'd consider this a method to generate unfolded conformations that probably have no relation to the true temperature denatured state. But let's be honest, you're never going to come close to Boltzmann sampling of an unfolded state in 300 ns so why bother with the water?Your link ( http://manual.gromacs.org/online/protunf.html ) is only concerned with analysis, so it is irrelevant.If you are determined to use NPT then I suppose that you could use the Berendsen barostat (more stable in simulations but you get the wrong ensemble) with a very low compressibility. That's about all I can say, perhaps somebody else will comment.Good luck,Chris.-- original message --Dear Chris,Thank you for your reply.My protein is very stable.I simulated it in 300ns in 300K before but there was almost no change.That's why I want to do denaturation now.I want to start a new simulation on the protein which is unfolded.And I'll read the paper you told me.Thank you.But I don't understand what you recommend me to do.You use 3000K on your protein and the protein unfolded.I use 600K on my protein but the system explode(box become very big and protein locate at corner).I saw the second way on this web,http://manual.gromacs.org/online/protunf.htmlBut it also useless to me.And in my mdp I use thermostat and barostat, which means my system is NPT.Does anything wrong in my methods?Sincerely yours,Hsin-Lin--gmx-users mailing list gmx-users@gromacs.orghttp://lists.gromacs.org/mailman/listinfo/gmx-usersPlease search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org.can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] Heat Capacity Question
Hello, I am trying to compare the heat capacity (at NPT) of 1000 molecules of methanol. I ran it all to equilibrium and used g_energy and -nmol 1000 to calculate the heat capacity. The value I achieved, ~140 J/mol*K is far from what I see is 79.5 J/mol. I have read on some past posts that there was some bug in calculating heat capacity but I'm not sure if that applies. I tried plotting Enthalpy vs Temp inorder to get dH/dT since that should be equal to heat capacity but I'm getting ~140 J/mol*K. I'm not sure if I need to include the number of constraints and how would I do that. I used constr=all-bonds. Is there something I'm doing wrong? when it says 140 J/mol*K, it is per mole of what? I had calculated heat of vaporization using Epotg - Epotliq+RT=Hvap and I got it close to the experimental value (34.09 compared to 35.2 kJ/mol). Thanks for the help. -- *Best regards,* ** *Fabian F. Casteblanco* *Rutgers University -- * *Chemical Engineering PhD Student* *C: +908 917 0723* *E: **fabian.castebla...@gmail.com* fabian.castebla...@gmail.com -- 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] Including a solvation model after converting from AMBER to GROMACS
Hello, I first used Antechamber and Leap to generate the topology and coordinate files for benzamide.pdb. I then converted them to gromacs formats and added the water molecules using the following commands: editconf -f benz.gro -bt dodecahedron -d 1.2 -o benz_box.gro genbox -cp benz_box.gro -cs tip4p.gro (there was no tip3p.gro) -p benz.top -o benz_solvated.gro * ; benz.top created by rdparm2gmx.pl Wed Jun 8 14:58:07 MDT 2011 [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ;name bond_typemasscharge ptype sigma epsilon n n 0. 0. A 3.25000e-01 7.11280e-01 c c 0. 0. A 3.39967e-01 3.59824e-01 haha 0. 0. A 2.59964e-01 6.27600e-02 hnhn 0. 0. A 1.06908e-01 6.56888e-02 caca 0. 0. A 3.39967e-01 3.59824e-01 o o 0. 0. A 2.95992e-01 8.78640e-01 [ moleculetype ] ; Namenrexcl solute 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB 1 ca 1MOL C 1 -0.07700 12.00 2 ca 1MOL C1 2 -0.13800 12.00 3 ca 1MOL C2 3 -0.10900 12.00 4 ca 1MOL C3 4 -0.13900 12.00 5 ca 1MOL C4 5 -0.10500 12.00 6 ca 1MOL C5 6 -0.14160 12.00 7 c 1MOL C6 70.67070 12.00 8 o 1MOL O 8 -0.61010 16.00 9 n 1MOL N 9 -0.67400 14.00 10 ha 1MOL H 100.15600 1.00 11 ha 1MOL H1 110.13800 1.00 12 ha 1MOL H2 120.13500 1.00 13 ha 1MOL H3 130.13600 1.00 14 ha 1MOL H4 140.13300 1.00 15 hn 1MOL H5 150.31750 1.00 16 hn 1MOL H6 160.30750 1.00 [ bonds ] ; aiaj funct r k 110 1 1.0870e-01 2.8811e+05 211 1 1.0870e-01 2.8811e+05 312 1 1.0870e-01 2.8811e+05 413 1 1.0870e-01 2.8811e+05 514 1 1.0870e-01 2.8811e+05 915 1 1.0090e-01 3.4326e+05 916 1 1.0090e-01 3.4326e+05 1 2 1 1.3870e-01 4.0033e+05 1 6 1 1.3870e-01 4.0033e+05 2 3 1 1.3870e-01 4.0033e+05 3 4 1 1.3870e-01 4.0033e+05 4 5 1 1.3870e-01 4.0033e+05 5 6 1 1.3870e-01 4.0033e+05 6 7 1 1.4870e-01 2.9263e+05 7 8 1 1.2140e-01 5.4225e+05 7 9 1 1.3450e-01 4.0016e+05 [ pairs ] ; aiaj funct 1 12 1 1 14 1 2 13 1 10 3 1 3 14 1 4 11 1 5 12 1 10 5 1 6 11 1 6 13 1 6 15 1 6 16 1 10 7 1 7 14 1 8 15 1 8 16 1 10 11 1 11 12 1 12 13 1 13 14 1 1 4 1 1 8 1 1 9 1 2 5 1 2 7 1 6 3 1 4 7 1 5 8 1 5 9 1 [ angles ] ; aiajak funct theta cth 1 211 1 1.2001e+02 4.0551e+02 2 110 1 1.2001e+02 4.0551e+02 2 312 1 1.2001e+02 4.0551e+02 3 211 1 1.2001e+02 4.0551e+02 3 413 1 1.2001e+02 4.0551e+02 4 312 1 1.2001e+02 4.0551e+02 4 514 1 1.2001e+02 4.0551e+02 5 413 1 1.2001e+02 4.0551e+02 6 110 1 1.2001e+02 4.0551e+02 6 514 1 1.2001e+02 4.0551e+02 7 915 1 1.1846e+02 4.1179e+02 7 916 1 1.1846e+02 4.1179e+02 15 916 1 1.1785e+02 3.3246e+02 1 2 3 1 1.1997e+02 5.6216e+02 1 6 5 1 1.1997e+02 5.6216e+02 1 6 7 1 1.2014e+02 5.4091e+02 2 1 6 1 1.1997e+02 5.6216e+02 2 3 4 1 1.1997e+02 5.6216e+02 3 4 5 1 1.1997e+02 5.6216e+02 4 5 6 1 1.1997e+02 5.6216e+02 5 6 7 1 1.2014e+02 5.4091e+02 6 7 8 1 1.2344e+02 5.7463e+02 6 7 9 1 1.1514e+02 5.7296e+02 8 7 9 1 1.2203e+02 6.3455e+02 [ dihedrals ] ;i j k l funcC0 ... C5 12312
[gmx-users]gmx4.5.4 genion problem: No line with moleculetype 'SOL' found
Hi, everyone: I am a new user of Gromacs, and I am running through the tutorial. When I am trying to run the ligand-receptor binding tutorial from http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html I met some trouble in adding ion. Each time when I use genion, it shows: Will try to add 0 NA ions and 6 CL ions. Select a continuous group of solvent molecules Group 0 ( System) has 33046 elements Group 1 (Protein) has 1693 elements Group 2 ( Protein-H) has 1301 elements Group 3 (C-alpha) has 163 elements Group 4 ( Backbone) has 489 elements Group 5 ( MainChain) has 653 elements Group 6 ( MainChain+Cb) has 805 elements Group 7 (MainChain+H) has 815 elements Group 8 ( SideChain) has 878 elements Group 9 (SideChain-H) has 648 elements Group10 (Prot-Masses) has 1693 elements Group11 (non-Protein) has 31353 elements Group12 ( Other) has15 elements Group13 (JZ4) has15 elements Group14 ( Water) has 31338 elements Group15 (SOL) has 31338 elements Group16 ( non-Water) has 1708 elements Select a group: 15 Selected 15: 'SOL' Number of (3-atomic) solvent molecules: 10446 Processing topology Back Off! I just backed up temp.top to ./#temp.top.3# --- Program genion_d, VERSION 4.5.4 Source code file: gmx_genion.c, line: 285 Fatal error: No line with moleculetype 'SOL' found the [ molecules ] section of file 'topol.top' I checked my topology file and it looks fine: ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include gromos43a1.ff/spc.itp ; Include ligand topoloty #include drg.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include gromos43a1.ff/ions.itp [ system ] ; Name Protein [ molecules ] ; Compound#mols Protein_chain_A 1 JZ4 1 SOL 10446 One thing that might happen is in the genion source file, I read through it, and the problem either happens in loading the line to buf2, or in the gmx_strcmp(buf2,SOL), since clearly the SOL_line is -1 aftermath. The other thing I tried is to remove the ligand JZ4 part in both topology and coordinates file, and in this case, it works perfectly for adding ion. But in this way, I do not know how to insert my ligand into the system since it might collide with solvent. Can someone help me with this problem? Thank you all very much. Ye Yang -- 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_hbond
Hi, To help clarify my previous g_hbond question, I have these two groups in my index file [ a_100_a_101] # 100 is N, #101 is H 100 101 [ a_200 ] # 200 is O 200 when I ran g_hbond, I got Found 1 donors and 2 acceptors. The part that I don't quite understand is why it says 2 acceptors. Did I set up the groups correctly? Again, hope this clarifies my question. Thanks for your insight. Simon -- 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_hbond
From g_hbond -h OH and NH groups are regarded as donors, O is an acceptor always, N is an acceptor by default, but this can be switched using -nitacc. Dummy hydrogen atoms are assumed to be connected to the first preceding non-hydrogen atom. The two groups are to find hbonds between group A and group B. If you want to find hbonds within group A, then you specify an index group that contains group A two times. I think that you want: [ group ] 100 101 200 Then give group 2x as the identical index group. PS, there were problems with g_hbond a few months ago reported on list, I suggest that you check to ensure that these problems were fixed. Chris. -- original message -- Hi, To help clarify my previous g_hbond question, I have these two groups in my index file [ a_100_a_101] # 100 is N, #101 is H 100 101 [ a_200 ]# 200 is O 200 when I ran g_hbond, I got Found 1 donors and 2 acceptors. The part that I don't quite understand is why it says 2 acceptors. Did I set up the groups correctly? Again, hope this clarifies my question. Thanks for your insight. Simon -- 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: Gromacs error
Hi, I have installed gromacs 4.5 on fedora core 15 and whenever I try to run any command like pdb2gmx ... I am getting the following error : error while loading shared libraries: libgmx.so.6: cannot enable executable stack as shared object requires: Permission denied Pls help?? -- Bharat -- 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: Gromacs error
Someone with some more in depth knowledge will hopefully pipe up, but until then there are some things you can read up on and see if it will solve your issue. Google is your friend. Put error while loading shared libraries: libgmx.so.6: Permission denied into it, and you get a number of topics on forums discussing the issue you have had. Not directly with libgmx.so.6 but that issue appears to be the same. And they all relate to Fedora from what I can see. This one appears to solve the issue - http://forums.fedoraforum.org/showthread.php?t=253870 With some more reading you should be able to sort out what the issue actually is, seems to be something to do with how files are handled with Fedora, and then the correct course of action. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of bharat gupta Sent: Friday, 17 June 2011 10:40 AM To: Discussion list for GROMACS users Subject: [gmx-users] Re: Gromacs error Hi, I have installed gromacs 4.5 on fedora core 15 and whenever I try to run any command like pdb2gmx ... I am getting the following error : error while loading shared libraries: libgmx.so.6: cannot enable executable stack as shared object requires: Permission denied Pls help?? -- Bharat -- 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] Gromacs to Amber trajectory
On 17/06/2011 2:57 AM, Raja Pandian wrote: Dear All, I have created Amber input file (.prmtop and .rst7) using Xleap. And then I have converted this input file into Gromacs input file format (*.gro and *.top) with amb2gmx.pl http://amb2gmx.pl script. I did simulation using Gromacs Package (Amber Force Field). Now I would like to convert Gromacs trajectory file to Amber trajectory file format. So that I can easily analyses this trajectory. I tried to convert Gromacs trajectory file to Amber trajectory file using VMD. This VMD converted trajectory is not working fine. Pls help me in this regards You really haven't said what you've done at the critical point, nor why you think it is not working. So we are unable to help at this time. Maek -- 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] gmx4.5.4 genion problem: No line with moleculetype 'SOL' found
Ye Yang wrote: Hi, everyone: I am a new user of Gromacs, and I am running through the tutorial. When I am trying to run the ligand-receptor binding tutorial from http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html I met some trouble in adding ion. Each time when I use genion, it shows: Will try to add 0 NA ions and 6 CL ions. Select a continuous group of solvent molecules Group 0 ( System) has 33046 elements Group 1 (Protein) has 1693 elements Group 2 ( Protein-H) has 1301 elements Group 3 (C-alpha) has 163 elements Group 4 ( Backbone) has 489 elements Group 5 ( MainChain) has 653 elements Group 6 ( MainChain+Cb) has 805 elements Group 7 (MainChain+H) has 815 elements Group 8 ( SideChain) has 878 elements Group 9 (SideChain-H) has 648 elements Group10 (Prot-Masses) has 1693 elements Group11 (non-Protein) has 31353 elements Group12 ( Other) has15 elements Group13 (JZ4) has15 elements Group14 ( Water) has 31338 elements Group15 (SOL) has 31338 elements Group16 ( non-Water) has 1708 elements Select a group: 15 Selected 15: 'SOL' Number of (3-atomic) solvent molecules: 10446 Processing topology Back Off! I just backed up temp.top to ./#temp.top.3# --- Program genion_d, VERSION 4.5.4 Source code file: gmx_genion.c, line: 285 Fatal error: No line with moleculetype 'SOL' found the [ molecules ] section of file 'topol.top' Something doesn't match up here - the command backs up temp.top, but then complains it can't find SOL in topol.top. Either genion is looking at the wrong file or your command is somehow wrong. I checked my topology file and it looks fine: ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include gromos43a1.ff/spc.itp ; Include ligand topoloty #include drg.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include gromos43a1.ff/ions.itp [ system ] ; Name Protein [ molecules ] ; Compound#mols Protein_chain_A 1 JZ4 1 SOL 10446 One thing that might happen is in the genion source file, I read through it, and the problem either happens in loading the line to buf2, or in the gmx_strcmp(buf2,SOL), since clearly the SOL_line is -1 aftermath. The other thing I tried is to remove the ligand JZ4 part in both topology and coordinates file, and in this case, it works perfectly for adding ion. But in this way, I do not know how to insert my ligand into the system since it might collide with solvent. If removal of the JZ4 line relieves the problem, perhaps there's a problem with that line, i.e. the line ending? What type of system are you using? Sometimes Windows line endings cause problems. Always use a plain text editor and use dos2unix to process text files if you're on Windows. Otherwise, the work-around is to not have genion work on the topology. Make the corrections yourself. Simple addition of ions and subtraction of water molecules is trivial. -Justin Can someone help me with this problem? Thank you all very much. Ye Yang -- 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] Re: Gromacs error
thanks.. I fixed the problem by using the command execstack -c filename but I have another issue .. I am am preparing the structure for simulation which is a docked complex containing Phospharylated tyrosine. I am using Amber 99 force field and update the residuetypes.dat, aminoacid.rtp, ffbonded.itp files for pTYR but still the error that Residue 'PTYR' not found in residue topology database ... but all the changes I have made then where else could the problem be ?? On Fri, Jun 17, 2011 at 10:04 AM, Dallas Warren dallas.war...@monash.eduwrote: Someone with some more in depth knowledge will hopefully pipe up, but until then there are some things you can read up on and see if it will solve your issue. ** ** Google is your friend. ** ** Put “error while loading shared libraries: libgmx.so.6: Permission denied” into it, and you get a number of topics on forums discussing the issue you have had. Not directly with libgmx.so.6 but that issue appears to be the same. And they all relate to Fedora from what I can see. ** ** This one appears to solve the issue - http://forums.fedoraforum.org/showthread.php?t=253870 ** ** With some more reading you should be able to sort out what the issue actually is, seems to be something to do with how files are handled with Fedora, and then the correct course of action. ** ** Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. ** ** *From:* gmx-users-boun...@gromacs.org [mailto: gmx-users-boun...@gromacs.org] *On Behalf Of *bharat gupta *Sent:* Friday, 17 June 2011 10:40 AM *To:* Discussion list for GROMACS users *Subject:* [gmx-users] Re: Gromacs error ** ** Hi, I have installed gromacs 4.5 on fedora core 15 and whenever I try to run any command like pdb2gmx ... I am getting the following error : error while loading shared libraries: libgmx.so.6: cannot enable executable stack as shared object requires: Permission denied Pls help?? -- Bharat -- 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 -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- 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] load imbalance
Hi all, I am trying to run GB model simulation of a small protein. I keep getting these errors for every step printed to the log file. DD load balancing is limited by minimum cell size in dimension X DD step 35999 vol min/aver 0.799! load imb.: force 154.9% Below i copied my mdp parameters. I'd appreciate any suggestion to help me fix this. Thanks, Nihal integrator = sd tinit= 0 dt = 0.002 nsteps = 500 simulation_part = 1 init_step= 1 %start from 5ns nstxout = 5000 nstvout = 5000 nstenergy= 500 nstxtcout= 500 nstlog = 500 xtc_grps = System energygrps = System comm_mode= Linear ; neighbor searching and vdw/pme setting up nstlist = 10 ns_type = grid pbc = xyz rlist= 2.0 coulombtype = pme fourierspacing = 0.1 pme_order= 6 rcoulomb = 2.0 vdwtype = Cut-off rvdw_switch = 1.0 rvdw = 2.0 ; cpt control tcoupl = Berendsen tc-grps = System tau_t= 0.1 ref_t= 300.0 Pcoupl = Berendsen pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ; velocity temperature control gen_vel = yes gen_temp = 300.0 annealing= no constraints = hbonds constraint_algorithm = lincs morse= no -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu -- 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] load imbalance
On 17/06/2011 12:44 PM, E. Nihal Korkmaz wrote: Hi all, I am trying to run GB model simulation of a small protein. I keep getting these errors for every step printed to the log file. DD load balancing is limited by minimum cell size in dimension X DD step 35999 vol min/aver 0.799! load imb.: force 154.9% Not all systems can efficiently parallelize on arbitrary numbers of processors for a given implementation. There's an analysis at the top of the .log file that describes the issues leading to the minimum cell size. Possibly there's an issue there, but more likely you've got not enough work for your processors. Mark Below i copied my mdp parameters. I'd appreciate any suggestion to help me fix this. Thanks, Nihal integrator = sd tinit= 0 dt = 0.002 nsteps = 500 simulation_part = 1 init_step= 1 %start from 5ns nstxout = 5000 nstvout = 5000 nstenergy= 500 nstxtcout= 500 nstlog = 500 xtc_grps = System energygrps = System comm_mode= Linear ; neighbor searching and vdw/pme setting up nstlist = 10 ns_type = grid pbc = xyz rlist= 2.0 coulombtype = pme fourierspacing = 0.1 pme_order= 6 rcoulomb = 2.0 vdwtype = Cut-off rvdw_switch = 1.0 rvdw = 2.0 ; cpt control tcoupl = Berendsen tc-grps = System tau_t= 0.1 ref_t= 300.0 Pcoupl = Berendsen pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ; velocity temperature control gen_vel = yes gen_temp = 300.0 annealing= no constraints = hbonds constraint_algorithm = lincs morse= no -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu mailto:kork...@wisc.edu -- 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] monitoring the water molecules
Hi gmx-users. I am doing MD simulation with the green fluorescent protein, where confined water molecules exist inside the protein barrel. During the coarse of the simulation i noticed these confined water molecule get exchange with outside bulk water. Is it possible to monitor or mark the water molecules during the simulations? For my analysis it would be very much useful. Can anyone guide me? Thanks Rama -- 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] Gromacs to Amber trajectory
Dear All, I have created Amber input file (.prmtop and .rst7) using Xleap. And then I have converted this input file into Gromacs input file format (*.gro and *.top) with amb2gmx.pl script. I did simulation using Gromacs Package (Amber Force Field). Now I would like to convert Gromacs trajectory file to Amber trajectory file format. So that I can easily analyses this trajectory. I tried to convert Gromacs (.xtc) trajectory file to Amber (.mdcrd) trajectory file using VMD. This VMD converted trajectory is not working fine for DCCM (Dynamic cross correlation Matrix) analysis. Now i'm trying to convert Gromacs trajectory into dcd format, and then use ptraj to read the dcd file and write the mdcrd (or AMBER netcdf) trajectory. Example: --- [1] Gromacs20ns.xtc à nojump.xtc (using trjcat/trjconv) [2] nojump.xtc à amber20ns.dcd (using VMD) [3] Ptraj file conversion trajin amber20ns.dcd trajout amber20ns.nc netcdf (or) Is it necessary to do image for this file. trajin test.dcd center origin image origin center trajout amber20ns.nc netcdf Is this correct procedure? I want to do DCCM (Dynamic cross correlation analysis). DCCM Ptraj file trajin test.rst7 trajin amber20ns.nc strip :WAT strip :Cl- center :1-85 origin image origin center matrix correl name corr @CA out amber20ns.dccm byres If you have any ptraj file format for this. Actually i did simulation based on NPT ensemble. Is it necessary to mention the BOX dimensions in any were in the dcd file creation? Already i tried to convert Gromacs trajectory into PDB (total trajectory) but it is not working well for the analysis purpose of AMBER. Eagerly waiting for your suggestion Regards Raja On Fri, Jun 17, 2011 at 6:46 AM, Mark Abraham mark.abra...@anu.edu.auwrote: ** On 17/06/2011 2:57 AM, Raja Pandian wrote: Dear All, I have created Amber input file (.prmtop and .rst7) using Xleap. And then I have converted this input file into Gromacs input file format (*.gro and *.top) with amb2gmx.pl script. I did simulation using Gromacs Package (Amber Force Field). Now I would like to convert Gromacs trajectory file to Amber trajectory file format. So that I can easily analyses this trajectory. I tried to convert Gromacs trajectory file to Amber trajectory file using VMD. This VMD converted trajectory is not working fine. Pls help me in this regards You really haven't said what you've done at the critical point, nor why you think it is not working. So we are unable to help at this time. Maek -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] monitoring the water molecules
On 17/06/2011 12:55 PM, Ramachandran G wrote: Hi gmx-users. I am doing MD simulation with the green fluorescent protein, where confined water molecules exist inside the protein barrel. During the coarse of the simulation i noticed these confined water molecule get exchange with outside bulk water. Is it possible to monitor or mark the water molecules during the simulations? For my analysis it would be very much useful. Can anyone guide me? Thanks They have the same atom number throughout. Whatever you want to do can be done using them, possibly via g_select creating dynamic selection groups. 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
[gmx-users] Re: gmx-users Digest, Vol 86, Issue 97
Dear Sir, Above error was solved but the system has raised a following new error, i.e., Fatal error: 52 atoms are not part of any of the T-Coupling groups How do I find which atom file has problem? help me to solve this problem... -- ** Ithayaraja M, Research Scholar, Department of Bionformatics, Bharathiar University, Coimbatore 641 046, Tamil Nadu India -- 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] cross correlations
Dear all, Is there any built in function that gives me the pairwise correlation of the fluctuation (unit vector between two coordinates of a residue) of residues (averaged over the input trajectory). I tried g_covar but that's not what i'm looking for. The result I want should be an NxN matrix with values ranging from -1 to 1. Thanks in advance, Nihal -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu -- 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
