Re: [gmx-users] Fatal Error: Residue 'DMP' not found in residue topology database

On 9/20/13 2:28 AM, Santhosh Kumar Nagarajan wrote: Hi guys, The error I'm getting is as follows "All occupancies are one Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomtypes.atp Atomtype 1 Reading residue database... (oplsaa) Opening force field file /usr/local/g

Re: [gmx-users] fatal error with charmm/amber forcefield

On Wed, Jul 31, 2013 at 11:20 PM, Sanku M wrote: > Dear Gromacs users, > I am using gromacs 4.5.4 . > Is there any known issue/problem in running hamiltonian replica exchange > calculations or FEP with charm27.ff or amber forcefield in gromacs4.5.4 ? Almost certainly. Do check out the relea

Re: [gmx-users] Fatal error: Failed to lock: md.log. Function not implemented.

On 4/29/13 9:30 PM, maggin wrote: Hi, when I use GROMACS4.5.5 to do peptid simulation. At NVT step, system is not equilibration, so I extend NVT simulation as follows: tpbconv -s nvt.tpr -extend 2000 -o next1.tpr mpirun -np 4 mdrun_mpi -reprod -s next1.tpr -cpi nvt.cpt after finish this e

Re: [gmx-users] Fatal error: Number of atoms in Topology is not the same as in Trajectory

ion list for GROMACS users Sent: Monday, January 28, 2013 2:32 PM Subject: Re: [gmx-users] Fatal error: Number of atoms in Topology is not the same as in Trajectory http://www.gromacs.org/Documentation/Terminology/Blowing_Up contains the ideas that will likely help you, e.g. smaller time step, more eq

Re: [gmx-users] Fatal error: Number of atoms in Topology is not the same as in Trajectory

ssion list for GROMACS users Sent: Monday, January 28, 2013 2:32 PM Subject: Re: [gmx-users] Fatal error: Number of atoms in Topology is not the same as in Trajectory http://www.gromacs.org/Documentation/Terminology/Blowing_Up contains the ideas that will likely help you, e.g. smaller time step,

Re: [gmx-users] Fatal error: Could not find frame with time

thank u Mark * Regards** N.T. Devika* On Tue, Jan 29, 2013 at 1:43 PM, Mark Abraham wrote: > On Tue, Jan 29, 2013 at 8:24 AM, Devika N T > wrote: > > > *Hi All > > > > * > > *I have completed 2ns simulation and I was extending my simu**lation for > > 1ns. > > * > > * > > > > Command _

Re: [gmx-users] Fatal error: Could not find frame with time

On Tue, Jan 29, 2013 at 8:24 AM, Devika N T wrote: > *Hi All > > * > *I have completed 2ns simulation and I was extending my simu**lation for > 1ns. > * > * > > Command _ Given _for_extension:* > > tpbconv -s Ca_CaM_2ns.tpr -f Ca_CaM_2ns.trr -e Ca_CaM_2ns.edr -extend 1000 > -o Ca_CaM_3ns.tpr > >

Re: [gmx-users] Fatal error: Number of atoms in Topology is not the same as in Trajectory

ible problems > might be considered? > > > Thanks for your suggestions. > > Sincerely, > Shima > > > > From: Justin Lemkul > To: Discussion list for GROMACS users > Sent: Sunday, January 6, 2013 9:15 AM > Subject: Re

Re: [gmx-users] Fatal error: Number of atoms in Topology is not the same as in Trajectory

sugestions? What are the possible problems might be considered? Thanks for your suggestions. Sincerely, Shima From: Justin Lemkul To: Discussion list for GROMACS users Sent: Sunday, January 6, 2013 9:15 AM Subject: Re: [gmx-users] Fatal error: Number of

Re: [gmx-users] Fatal error: Number of atoms in Topology is not the same as in Trajectory

On 1/6/13 1:00 AM, Shima Arasteh wrote: I ran NPT equilibration for 1ns. Would that be ok if I rerun it for 1 or more ns ? I have no idea what will be necessary for your system. That's up to you to analyze and determine. -Justin -- Justin A. Le

Re: [gmx-users] Fatal error: Number of atoms in Topology is not the same as in Trajectory

I ran NPT equilibration for 1ns. Would that be ok if I rerun it for 1 or more ns ?   Sincerely, Shima - Original Message - From: Justin Lemkul To: Discussion list for GROMACS users Cc: Sent: Sunday, January 6, 2013 9:15 AM Subject: Re: [gmx-users] Fatal error: Number of atoms in

Re: [gmx-users] Fatal error: Number of atoms in Topology is not the same as in Trajectory

On 1/6/13 12:33 AM, Shima Arasteh wrote: Do you mean that I re-run NPT step with the new index file and npt.gro (which I got from the last NPT equilibration)? That's not clear to me yet. That's where I'd start. You may have to run the new configuration through the entire equilibration pro

Re: [gmx-users] Fatal error: Number of atoms in Topology is not the same as in Trajectory

users Sent: Saturday, January 5, 2013 9:49 PM Subject: Re: [gmx-users] Fatal error: Number of atoms in Topology is not the same as in Trajectory On 1/5/13 3:46 AM, Shima Arasteh wrote: > Dear all, > > I have a system of POPC/Protein/water/ions to simulate. I am trying to > simula

Re: [gmx-users] Fatal error: Number of atoms in Topology is not the same as in Trajectory

On 1/5/13 3:46 AM, Shima Arasteh wrote: Dear all, I have a system of POPC/Protein/water/ions to simulate. I am trying to simulate this system by getting ideas from Justin's tutorial of kalp15-dppc. I've passed all steps of EM, NVT, and NPT as I expected. But when I want to run mdrun, I get s

Re: [gmx-users] Fatal Error with AMBER03

On 12/14/12 2:22 PM, Eduardo Oliveira wrote: Hi, I'm trying to use AMBER03 force field with my protein but when i run pdb2gmx i get a fatal error message: Fatal error: Incomplete ring in HIS415 The problem is, when I open the structure on pymol i can't see any missing atoms. Does anybody h

Re: [gmx-users] Fatal Error with AMBER03

Hi Eduardo, Some visualization softwares completes the structure, even if it's broken. I suggest you to look at the .pdb file directly in notepad and check out the composition of your HIS415. Regards -- Marcelo Depólo Polêto Molecular Animal Infectology Laboratory - LIMA Department of Biochemis

Re: [gmx-users] Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus

On 2012-11-18 10:40, Atila Petrosian wrote: Dear David Thanks for your attention. I have 2 problems/questions: 1) There are a specific orientation for GLN ligand with regard to protein in my system. If I do what you said [you make a separate molecule Gln-Ala using pymol or vmd], specific orien

Re: [gmx-users] Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus

On 2012-11-17 16:26, Atila Petrosian wrote: Dear David Thanks for your quick reply. You said "Add an alanine after the gln then in the top file rename and remove atoms". I confused. Why ALA? ALA (alanine) is a residue which is very simple than GLN structurally. I should add alanine after the

Re: [gmx-users] Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus

On 2012-11-17 15:37, Atila Petrosian wrote: Hi all. After using amber03 force field for protein-ligand simulation (pdb2gmx), I encountered with following error: Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus. Ligand in my system is a single res

Re: [gmx-users] Fatal error: Atomtype F not found

On 2012-10-04 04:39, Nur Syafiqah Abdul Ghani wrote: Dear Users, Right now i already done for creating the a gro file from antechamber to gromacs format of my molecule which is hexafluoroisopropanol. But when i want to minimize it in vacuum it show atomtype F not found. Im using oplsaa force fie

Re: [gmx-users] Fatal error: Atomtype F not found

On 10/3/12 10:43 PM, Nur Syafiqah Abdul Ghani wrote: Dear Users, Right now i already done for creating the a gro file from antechamber to gromacs format of my molecule which is hexafluoroisopropanol. But when i want to minimize it in vacuum it show atomtype F not found. Im using oplsaa force f

Re: [gmx-users] Fatal error during lipid bilayer minimization

On 13/09/2012 4:33 PM, Bharath K. Srikanth wrote: Hi I am trying to simulate the self-assembly of course-grained DSPC lipids into a lipid bilayer. I made a box (7.5 x 7.5 x 7.5) containing 128 DSPC lipids, and added 768 molecules of water to the system, and ran a minimization (using em.mdp). The

Re: [gmx-users] Fatal error: Number of grid cells is zero. Probably the system and box collapsed.

On 1/08/2012 1:06 PM, leila karami wrote: Dear gromacs user I did simulation of carbon nanotube (one in center and 6 in the vicinity of that)|: every CNT have 120 atoms. 1) energy minimization 2) equilibration in NVT ensemble when I did equilibration in NPT ensemble, I encountered Fatal error

Re: [gmx-users] FATAL ERROR: Residue "LIG" not found in residue topology database.

On 7/31/12 7:48 AM, Ali Alizadeh wrote: Dear All usres: I am trying to do a simple system that contains 4 molecules ethane and MD run using GROMACS. I build my .pdb file by using Avogadro software . Afterwards, I try to generate the topology and .gro file using pdb2gmx program and it generates

Re: [gmx-users] Fatal error: Atomtype O2 not found

On 6/9/12 7:24 AM, ramaraju801 wrote: hi am working on a DNA-protein complex, during the energy minimization step its giving the following error, "Fatal error: Atomtype O2 not found" am using charmm27 force field and used the command "grompp -f minim.mdp -c protein.gro -p protein.top -o prote

Re: [gmx-users] Fatal error: atom C not found in buiding block 19NH2 while combining tdb and rtp

On 5/23/12 1:26 PM, ankita oindrila wrote: i am stimulting an AMP protein in water. this is the error i get on my first step.. pdb2gmx -f 1PG1_1.pdb -o 1PG1_1_processed.gro -water spce error: Fatal error: atom C not found in buiding block 19NH2 while combining tdb and rtp please HELP!!

Re: [gmx-users] fatal error: missing H atom in .pdb file

On 5/14/12 11:19 AM, Shima Arasteh wrote: Dear gmx users, I changed the aminoacids.rtp file recently. Now, when I run pdb2gmx, I get the fatal error: atom H is missing in residue For 0 in the pdb file You might need to add atom H to the hydrogen database of building block For in the file amin

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

:42 PM Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs On 14/05/2012 6:00 PM, Shima Arasteh wrote: Thanks for your suggestions. >Now, I think that it's better to add the N atom of next residue  to the .pdb >file and then add hydrogen atoms to its .

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

worth the time to write down. Mark Sincerely, Shima *From:* Justin A. Lemkul *To:* Discussion list for GROMACS users *Sent:* Sunday, May 13, 2012 9:40 PM *Subject:* Re: [gmx-users] Fatal error: No atoms found

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

ely, Shima From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Sunday, May 13, 2012 9:40 PM Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs On 5/13/12 12:42 PM, Shima Arasteh wrote: > OK, so I entered the H atom cor

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

--- *From:* Justin A. Lemkul *To:* Discussion list for GROMACS users *Sent:* Sunday, May 13, 2012 9:44 PM *Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs On 5/13/12 1:06 PM, Shima Arasteh wrote: > Even in gromos87, if I want to make a .rtp file for

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

for GROMACS users > *Sent:* Sunday, May 13, 2012 8:36 PM > *Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in > residue pairs > > > > On 5/13/12 11:43 AM, Shima Arasteh wrote: >  > Again thanks for all your replies. >  > As I got through yo

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

  Thanks, It was just a question and I prefer to use the CHARMM36. From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Sunday, May 13, 2012 9:44 PM Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs On 5

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

erive them yourself. -Justin Cheers, Shima *From:* Justin A. Lemkul *To:* Discussion list for GROMACS users *Sent:* Sunday, May 13, 2012 8:36 PM *Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

--- *From:* Justin A. Lemkul *To:* Discussion list for GROMACS users *Sent:* Sunday, May 13, 2012 8:36 PM *Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs On 5/13/12 11:43 AM, Shima Arasteh wrote: > Again thanks for all your replies. > As I got through

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

t for GROMACS users Sent: Sunday, May 13, 2012 8:36 PM Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs On 5/13/12 11:43 AM, Shima Arasteh wrote: > Again thanks for all your replies. > As I got through your advices, I found that the atoms contribut

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

:36 PM Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs On 5/13/12 11:43 AM, Shima Arasteh wrote: > Again thanks for all your replies. > As I got through your advices, I found that the atoms contribute in making > bonds > and angles in a resid

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

Shima *From:* Justin A. Lemkul *To:* Discussion list for GROMACS users *Sent:* Saturday, May 12, 2012 10:12 PM *Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs On 5/12/12 1:37 PM, Justin A. L

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

which I can get through the files of swissparam? Thanks in advance, and sorry for disturbing you friends. Shima From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Saturday, May 12, 2012 10:12 PM Subject: Re: [gmx-users] Fatal error: No atoms

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

All right. Thank you Sincerely, Shima From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Saturday, May 12, 2012 10:36 PM Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs On 5/12/12 2:00 PM, Shima

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

line ?:  [ dihedrals ]   O C   +N   CA Cheers, Shima From: Justin A. Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Sent: Saturday, May 12, 2012 10:07 PM Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

On 5/12/12 2:00 PM, Shima Arasteh wrote: The total charge is zero in real but what I got through swissparam is as below: [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 C=O 1 LIG C 1 0.4500 12.0110 2 O=C 1 LIG O 2 -0.5700 15.9994 3 HCMM 1 LIG H1 3 0.0600 1.0079 4 HCMM 1 LIG H2 4 0.0600

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

   +N   CA Cheers, Shima From: Justin A. Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Sent: Saturday, May 12, 2012 10:07 PM Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs On 5/12/12 1:32 PM, Shima

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

On 5/12/12 1:37 PM, Justin A. Lemkul wrote: On 5/12/12 1:32 PM, Shima Arasteh wrote: Dear gmx users, I want to simulate a peptide in water. The peptide has a formyl residue as the N-terminus. I got the parameters of it and then add it to the .rtp file of charmm36.ff as below: [ For ] [ ato

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

On 5/12/12 1:32 PM, Shima Arasteh wrote: Dear gmx users, I want to simulate a peptide in water. The peptide has a formyl residue as the N-terminus. I got the parameters of it and then add it to the .rtp file of charmm36.ff as below: [ For ] [ atoms ] ; name type charge chargegroup C C 0.4500

Re: [gmx-users] Fatal error

On 4/25/12 8:19 AM, seera suryanarayana wrote: Respected sir, While i am running the gromacs always i am getting the error "Residue 'GNP' not found in residue topology database".Kindly tell me the what the error means. http://www.gromacs.org/Documentation/Errors#Residue

Re: [gmx-users] Fatal error in popc simulation: Atomtype LC3 not found

On 4/25/12 2:07 AM, Shima Arasteh wrote: Dear gmx users, I want to simulate popc in water. What I have done is: 1.Build the popc.top file using the popc.itp parameters and including gmx.ff, lipid.itp and spce.itp in it as below; ; Include forcefield parameters #include "./gmx.ff/forcefield.it

Re: [gmx-users] fatal error: The solvent group non-Protein is not continuous

On 4/21/12 1:17 PM, Shima Arasteh wrote: Dear gmx users, I am a new user of gromacs. I solvated my protein in water. Now I want to neutralize the system. I added 2 CL ions to the system but when run the following command, get the fatal error: # genion -s ions.tpr -o monomer_solv_ions.gro -p

Re: [gmx-users] Fatal error: Bond atom type names can't be single digits

Sangita Kachhap wrote: Hello all I am new for gromacs. I have to do MD simulation of membrane protein docked with organic molecule. I have gerated top and itp for ligand using PRODRG server also generated top file for complex. Hopefully you're not relying on an unrefined PRODRG topology. Se

Re: [gmx-users] Fatal error: Atom CG is used in the topology database...

Andy Somogyi wrote: Any suggestions for programmatically repairing the pdb, i.e. Guessing the missing residue atoms and adding them at the appropriate coordinates? I tried vmd's autopsf, which works, but evidently vmd's implementation of charm27 is different than Gromac's, it adds atom types n

Re: [gmx-users] Fatal error: Atom CG is used in the topology database...

Any suggestions for programmatically repairing the pdb, i.e. Guessing the missing residue atoms and adding them at the appropriate coordinates? I tried vmd's autopsf, which works, but evidently vmd's implementation of charm27 is different than Gromac's, it adds atom types not present in Gromac'

Re: [gmx-users] Fatal error: Atom CG is used in the topology database...

On 2012-03-23 05:39:38PM -0400, Justin A. Lemkul wrote: > > > Andy Somogyi wrote: > > Hi All, > > > > I'm trying to generate topology for a PDB from viperdb, PDB ID 1DZL, > > http://viperdb.scripps.edu/info_page.php?VDB=1dzl > > > > using > > > > pdb2gmx -f 1dzl_full.pdb -o test.pdb -p test.

Re: [gmx-users] Fatal error: Atom CG is used in the topology database...

Andy Somogyi wrote: Hi All, I'm trying to generate topology for a PDB from viperdb, PDB ID 1DZL, http://viperdb.scripps.edu/info_page.php?VDB=1dzl using pdb2gmx -f 1dzl_full.pdb -o test.pdb -p test.top I've tried CHARMM27 and AMBER03 FFs, water none and I get the result: Fatal error: At

RE: [gmx-users] fatal error

It is possible that the system is unstable/exploding due atoms being too close to each other in the initial system. Andreas -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Gavin Melaugh Sent: 21 March 2012 15:45 To: Discussion l

Re: [gmx-users] fatal error occuring.

swati patel wrote: Hello Justin, Somehow I obtained ligand and protein topology in charmm force fields. After command grompp,I am getting an error "No such moleculetype LIG" where lig is my ligand abbreviation. Any suggestions for my error?? Have you done the proper tutorial material? T

Re: [gmx-users] fatal error occuring.

ibi2010...@iiita.ac.in wrote: Hello Justin, After setting up grompp command,i am getting an error "Atoms in the .top are not numbered consecutively from 1 (rather, atomnr = 1, while at->nr = 1179)".I am heading up step by step taking your aid. What should i do?How to correct it?? Without s

Re: [gmx-users] Fatal error in MPI_Allreduce upon REMD restart

On Thu, Oct 27, 2011 at 4:09 PM, Mark Abraham wrote: > On 28/10/2011 9:29 AM, Ben Reynwar wrote: >> >> I found a post on the devel list from a couple of weeks ago where a >> fix is given and it appears to work for me. >> The link is >> http://lists.gromacs.org/pipermail/gmx-developers/2011-October

Re: [gmx-users] Fatal error in MPI_Allreduce upon REMD restart

On 28/10/2011 9:29 AM, Ben Reynwar wrote: I found a post on the devel list from a couple of weeks ago where a fix is given and it appears to work for me. The link is http://lists.gromacs.org/pipermail/gmx-developers/2011-October/005405.html The fix does not appear to have been incorporated into

Re: [gmx-users] Fatal error in MPI_Allreduce upon REMD restart

I found a post on the devel list from a couple of weeks ago where a fix is given and it appears to work for me. The link is http://lists.gromacs.org/pipermail/gmx-developers/2011-October/005405.html The fix does not appear to have been incorporated into the 4.5.5 release. On Tue, Oct 25, 2011 at

Re: [gmx-users] Fatal error in MPI_Allreduce upon REMD restart

On 26/10/2011 6:06 AM, Szilárd Páll wrote: Hi, Firstly, you're not using the latest version and there might have been a fix for your issue in the 4.5.5 patch release. There was a bug in 4.5.5 that was not present in 4.5.4 that could have produced such symptoms, but it was fixed without creati

Re: [gmx-users] Fatal error in MPI_Allreduce upon REMD restart

Hi, Firstly, you're not using the latest version and there might have been a fix for your issue in the 4.5.5 patch release. Secondly, you should check the http://redmine.gromacs.org bugtracker to see what bugs have been fixed in 4.5.5 (ideally the target version should tell). You can also just do

Re: [gmx-users] Fatal Error: Constraints present with Normal Mode Analysis, this combination is not supported

On 21/09/2011 1:38 AM, Andrey Dyachenko wrote: Dear gmx-users, I am trying to perform the Normal Mode Analysis of 24 kDa protein in water. Here is the .mdp file I am using: integrator = nm dt = 0.002 nsteps = 1 emtol = 1 nstcomm

Re: [gmx-users] Fatal error when position restraint the coordinates-reg

On 31/08/2011 11:50 AM, ITHAYARAJA wrote: Dear sir, I found the following error, when I did the position restraint the coordinates after grompp. Fatal error: Too many LINCS warnings (1347) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set

Re: [gmx-users] Fatal error: file type out of range (48)

Carla Jamous wrote: Hi, Please does anyone Know what this error means? Fatal error: file type out of range (48) Here's my script: #PBS -S /bin/bash #PBS -N job_md6ns #PBS -e job_md6ns.err #PBS -o job_md6ns.log #PBS -m ae -M carlajam...@gmail.com #PBS -l selec

Re: [gmx-users] Fatal Error: The largest charge group contains 140 atoms. The maximum is 32

Lalit wrote: Hi All, At this time, I am very much interested in using gromacs utilities for analysis with {.dcd, .psf} files. Especially, eg., for g_density. Primarily, I use NAMD/VMD for my work. I am following this link from NAMD mailing list: http://www.ks.uiuc.edu/Research/namd/mailing

Re: [gmx-users] Fatal error: Not enough memory. Failed to realloc

shivangi nangia wrote: Dear gmx-users, I was carrying out a continuation of an NPT equilibration from NVT. As soon the job started it ran into the following error: Fatal error: Not enough memory. Failed to realloc 1488624 bytes for nl->shift, nl->shift=0x0 (called from file ns.c, line 101)

Re: [gmx-users] Fatal error: Atomtype CB not found

On 10/05/2011 3:10 AM, Justin A. Lemkul wrote: ITHAYARAJA wrote: Dear Sir Greetings! I am following every gromacs applications based on your manuals. I now get stuck in grompp -energy minimization step during generation of .tpr file for my ligand and protein. the error which i found is th

Re: [gmx-users] Fatal error: Atomtype CB not found

ITHAYARAJA wrote: Dear Sir Greetings! I am following every gromacs applications based on your manuals. I now get stuck in grompp -energy minimization step during generation of .tpr file for my ligand and protein. the error which i found is the following, Ignoring obsolete mdp entry 'titl

Re: [gmx-users] Fatal error: Attempting to read a checkpoint file of version 12 with code of version 4

On 1/05/2011 11:48 PM, Faezeh Kargar wrote: Thank you very much for your reply. could you please tell me if there is any way to solve this problem and restart running the code? If my theory is right, keep using the same installation of GROMACS 4.5. Talk to whoever manages your system about

Re: [gmx-users] Fatal error: Attempting to read a checkpoint file of version 12 with code of version 4

Thank you very much for your reply. could you please tell me if there is any way to solve this problem and restart running the code? Karagr > On 30/04/2011 11:37 PM, Faezeh Kargar wrote: >> >> >> > On 4/30/2011 7:22 PM, Faezeh Kargar wrote: >> >> >> >> Dear gmx users, >> >> >> >> My code stops

Re: [gmx-users] Fatal error: Attempting to read a checkpoint file of version 12 with code of version 4

On 30/04/2011 11:37 PM, Faezeh Kargar wrote: > On 4/30/2011 7:22 PM, Faezeh Kargar wrote: >> >> Dear gmx users, >> >> My code stops running because of electricity voltage oscillation. it >> happened for several times and each time I restarted running my code. >> but for this time with command >

Re: [gmx-users] Fatal error: Attempting to read a checkpoint file of version 12 with code of version 4

> On 4/30/2011 7:22 PM, Faezeh Kargar wrote: >> >> Dear gmx users, >> >> My code stops running because of electricity voltage oscillation. it >> happened for several times and each time I restarted running my code. >> but for this time with command >> >> mdrun -s topol.tpr -x >> traj.part0002

Re: [gmx-users] Fatal error: Attempting to read a checkpoint file of version 12 with code of version 4

On 4/30/2011 7:22 PM, Faezeh Kargar wrote: Dear gmx users, My code stops running because of electricity voltage oscillation. it happened for several times and each time I restarted running my code. but for this time with command mdrun -s topol.tpr -x traj.part0002.part0003.part0004.part00

Re: [gmx-users] Fatal error: number of coordinates in coordinate file does not match topology

On 16/04/2011 6:05 PM, ahmet yıldırım wrote: Dear Justin, I have 6 EDO and 1 TRS ligans. I created coordinate and .itp files for each EDO moleculeusing prodrg web server. Then I created 6 .itp files as EDO1.itp, EDO2.itp.EDO6.itp. Why? The fragment [molecules] EDO 6 is what specifies s

Re: [gmx-users] Fatal error: number of coordinates in coordinate file does not match topology

Dear Justin, I have 6 EDO and 1 TRS ligans. I created coordinate and .itp files for eachEDO molecule using prodrg web server. Then I created 6 .itp files as EDO1.itp, EDO2.itp.EDO6.itp. I changed residue numbers. But I have Fatal Error "moleculetype EDO is redefined". Am I on the wrong track?:

Re: [gmx-users] Fatal error: number of coordinates in coordinate file does not match topology

ahmet yıldırım wrote: Dear Justin, Thanks for your valuable helps. How should I rearranged the conf.gro file for 6 EDO ligand? is the following conf.gro mistake? Well, it's certainly not working, is it? You only have one EDO molecule shown here. Is this the only one? If it is, then y

Re: [gmx-users] Fatal error: number of coordinates in coordinate file does not match topology

Dear Justin, Thanks for your valuable helps. How should I rearranged the conf.gro file for 6 EDO ligand? is the following conf.gro mistake? *conf.gro:* MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE 5354 2GLN N1 1.458 -1.158 0.739 2GLN H12 1.520 -1.083 0.763 ... 485HO

Re: [gmx-users] Fatal error: number of coordinates in coordinate file does not match topology

ahmet yıldırım wrote: Dear Justin, I built .rtp entries for two ligands using (http://davapc1.bioch.dundee.ac.uk/prodrg/). I added to the topol.top the following parts: #include "TRS.itp" #include "EDO.itp" Well, either pdb2gmx built the molecules into your topology or you're #including

Re: [gmx-users] Fatal error: number of coordinates in coordinate file does not match topology

Dear Justin, I built .rtp entries for two ligands using ( http://davapc1.bioch.dundee.ac.uk/prodrg/). I added to the topol.top the following parts: #include "TRS.itp" #include "EDO.itp" TRS 1 EDO 6 Furthermore I added the number of atoms (20) in the second line of t

Re: [gmx-users] Fatal error: number of coordinates in coordinate file does not match topology

ahmet yıldırım wrote: Dear users, pdb2gmx -f xxx.pdb water:spc forcefield:43a1 editconf -f conf.gro -bt cubic -d 1.0 -o box.gro genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr *Fatal error:* number of coordinates in coordin

Re: [gmx-users] fatal error

Thank you very much 22 Ocak 2011 23:07 tarihinde Justin A. Lemkul yazdı: > > > ahmet yıldırım wrote: > >> please look at the attached file >> >> > I had no problem making a topology. > > $ pdb2gmx -f 3MOA.pdb -ter > > ... > Using the Gromos43a1 force field in directory gromos43a1.ff > ... > Sele

Re: [gmx-users] fatal error

ahmet yıldırım wrote: please look at the attached file I had no problem making a topology. $ pdb2gmx -f 3MOA.pdb -ter ... Using the Gromos43a1 force field in directory gromos43a1.ff ... Select start terminus type for GLU-659 0: NH3+ 1: NH2 2: None 0 Start terminus GLU-659: NH3+ Select e

Re: [gmx-users] fatal error

ahmet yıldırım wrote: Dear Justin, I manually specify termini. I choosed "None" but I have the same error. Fatal error: atom C not found in residue 13NH2 while combining tdb and rtp Please post your .pdb file. -Justin 22 Ocak 2011 00:45 tarihinde Justin A. Lemkul

Re: [gmx-users] fatal error

Dear Justin, I manually specify termini. I choosed "None" but I have the same error. Fatal error: atom C not found in residue 13NH2 while combining tdb and rtp 22 Ocak 2011 00:45 tarihinde Justin A. Lemkul yazdı: > > > ahmet yıldırım wrote: > >> Dear justin, >> >> I looked at the pdb file. N

Re: [gmx-users] fatal error

ahmet yıldırım wrote: Dear justin, I looked at the pdb file. No NH2 reside contains carbon atom. What should I do? In this case, you need to manually specify termini. Choose "None" to allow your capping groups to be built properly. -Justin 22 Ocak 2011 00:18 tarihinde Justin A. Lemku

Re: [gmx-users] fatal error

Dear justin, I looked at the pdb file. No NH2 reside contains carbon atom. What should I do? 22 Ocak 2011 00:18 tarihinde Justin A. Lemkul yazdı: > > > ahmet yıldırım wrote: > >> I think I need to edit the aminoacids.rtp file in gromos43a1.ff folder as >> far as I understand from mailing list.

Re: [gmx-users] fatal error

ahmet yıldırım wrote: I think I need to edit the aminoacids.rtp file in gromos43a1.ff folder as far as I understand from mailing list. I am using 43a1 forcefield. I do not understand what kind of changes should I do. You do not need to modify the .rtp file, you need to modify your coordina

Re: [gmx-users] fatal error

I think I need to edit the aminoacids.rtp file in gromos43a1.ff folder as far as I understand from mailing list. I am using 43a1 forcefield. I do not understand what kind of changes should I do. *the aminoacids.rtp file:* [ ACE ] [ atoms ] CA CH3 0.000 0 C C 0.380 1

Re: [gmx-users] fatal error

ahmet yıldırım wrote: Dear users, Gromacs 4.5.3 pdb2gmx -f xxx.pdb -water spc select Force Field:9 *Fatal error:* atom C not found in buiding block 13NH2 while combining tdb and rtp For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Do

Re: [gmx-users] Fatal error (g_polystat)

-- Chandan kumar Choudhury NCL, Pune INDIA On Fri, Dec 24, 2010 at 3:13 AM, Mark Abraham wrote: > On 24/12/2010 4:58 AM, Chandan Choudhury wrote: > > Hello all !! > > I have a 30 ns trajectory in two parts (0-20 & 20-30). I am using Gromacs > 4.0.7. I concatenated using trjcat (*echo 2 | trjco

Re: [gmx-users] Fatal error (g_polystat)

On 24/12/2010 4:58 AM, Chandan Choudhury wrote: Hello all !! I have a 30 ns trajectory in two parts (0-20 & 20-30). I am using Gromacs 4.0.7. I concatenated using trjcat (*echo 2 | trjconv -s md10-30.tpr -f 0-30.trr -o pbc_whole.trr -n index_grdf.ndx -nice 0*). That looks like subset creati

Re: [gmx-users] Fatal error when using do_dssp

- Original Message - From: zhongjin Date: Tuesday, August 31, 2010 18:23 Subject: [gmx-users] Fatal error when using do_dssp To: gmx-users@gromacs.org --- | > Hi, > I have installed the dsspcmbi, and then add " export DSSP=/home

Re: [gmx-users] Fatal Error - RMSD Calculation

deisy yurley rodriguez sarmiento wrote: Hi everyone, I want to calculate the RMSD, and a few minutes to start the calculation, appears that Fatal Error: calloc for bond_mat[i] (nelem=50001, elsize=4, file gmx_rms.c, line 650) I don't have any idea what is the problem. Sounds like a memory

RE: [gmx-users] Fatal error: No such moleculetype Cl

Okey, I found the solution, it is the IFDEF statements in ions.itp. OPLS does not have CL but a CL- and therefore when I changed to CL- in my $FILE.top, it went through smoothly. Cheers, From: xru...@live.com To: gmx-users@gromacs.org Date: Mon, 26 Jul 2010 06:58:57 + Subject: [gmx-users]

Re: [gmx-users] Fatal error:

Nilesh Dhumal wrote: Hello, I am trying to equilibrate my system, ionic liquids. Simulations stops with following error Fatal error: 1 of the 43778 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.32754 nm) or

Re: Re: Re: [gmx-users] “Fatal error in PMP I_Bcast: Other MPI error, …..” occurs whe n using the ‘particle decomposition’ option.

2010 14:17Subject: Re:  Re: [gmx-users] “Fatal error in PMPI_Bcast: Other MPI error, …..” occurs when using the ‘particle decomposition’ option.To: Discussion list for GROMACS users <gmx-users@gromacs.org>> Hi, Mark, >   > I’ve noticed about the minimum cell diameter restrict,

Re: Re: [gmx-users] “Fatal error in PMPI_Bca st: Other MPI error, …..” occurs when usi ng the ‘particle decomposition’ option.

...@sohu.comdate: Tuesday, June 1, 2010 21:59Subject: Re: [gmx-users] “Fatal error in PMPI_Bcast: Other MPI error, …..” occurs when using the ‘particle decomposition’ option.To: Discussion list for GROMACS users <gmx-users@gromacs.org>> > Hi, Mark,> Thanks for the reply! > It

Re: [gmx-users] Fatal error: Atom O in residue CO 1 not found in rtp entry with 3 atoms while sorting atoms

- Original Message - From: "Justin A. Lemkul" Date: Wednesday, June 2, 2010 6:18 Subject: Re: [gmx-users] Fatal error: Atom O in residue CO 1 not found in rtp entry with 3 atoms while sorting atoms To: Gromacs Users' List > > Nilesh Dhumal wrote: &g

Re: [gmx-users] Fatal error: Atom O in residue CO 1 not found in rtp entry with 3 atoms while sorting atoms

Nilesh Dhumal wrote: I have addes the "CO" residue. Coordinate file REMARK Accelrys Discovery Studio PDB file REMARK Created: Fri May 28 17:26:23 Eastern Daylight Time 2010 HETATM1 C1 CO 0 -1.044 -0.027 0.066 0.00 0.00 C HETATM2 O2 CO 0 -0.009

Re: [gmx-users] Fatal error: Atom O in residue CO 1 not found in rtp entry with 3 atoms while sorting atoms

I have addes the "CO" residue. Coordinate file REMARK Accelrys Discovery Studio PDB file REMARK Created: Fri May 28 17:26:23 Eastern Daylight Time 2010 HETATM1 C1 CO 0 -1.044 -0.027 0.066 0.00 0.00 C HETATM2 O2 CO 0 -0.009 0.642 -0.037 0.00 0.

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