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

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

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/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.rtp Residu

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

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

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 ? I tried running an hamiltonian replica exchange using charmm27.ff by interpolating A state and B

[gmx-users] Fatal error: No donor atom 780

Hi all, I wonder what could be the cause of such a fatal error when using g_hbond with -contact option. The two index group I chose have no overlap, but certain index group pairs worked while others did not and gave this fatal error. Thanks, Yun -- gmx-users mailing listgmx-users@gromacs.or

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

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

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 extending, I got files: traj.trr stat

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

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

m To: Discussion 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

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

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

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 some errors about waters can not be settle. 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

[gmx-users] Fatal Error with AMBER03

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 had the same problem? Regards, Eduardo -- gmx-us

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

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

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 residue (GLN). There are [GLN], [NGLN] and [CGLN]

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

[gmx-users] Fatal error during lipid bilayer minimization

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 summary of the results is below. Reached the maxim

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

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

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: Number of grid cells is zero. Probably the

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

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 an error. I am using the 43a1 force field.

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

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

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 an error. I am using the 43a1 force field.

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

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

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 protein-EM-vacuum.tpr " regards, ram --

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!!

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

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!! -- gmx-users mailing listgmx-users@gromacs.o

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

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

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 aminoacids.hdb -Is it may as a

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

GROMACS users Sent: Monday, May 14, 2012 12:42 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 &

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

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

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   0   

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

[gmx-users] Fatal error

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. Suryanarayana Seera, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailma

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

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

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.itp" ; Include water topology #include "./gmx

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

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

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 topol.top -nname CL -nn 2 fatal error: Th

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

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

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. But when I am generating .tpr file for a POPC system using grompp getting an error: creatin

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

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

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: Atom CG is used in the topo

RE: [gmx-users] fatal error

list for GROMACS users Subject: [gmx-users] fatal error Hi all I am trying to relax the density of an alcohol system that I have just set up, but after a certain period of time I get the following error Fatal error: The X-size of the box (6.800588) times the triclinic skew factor (1.00) is

[gmx-users] fatal error

Hi all I am trying to relax the density of an alcohol system that I have just set up, but after a certain period of time I get the following error Fatal error: The X-size of the box (6.800588) times the triclinic skew factor (1.00) is smaller than the number of DD cells (4) times the smallest

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

[gmx-users] fatal error occuring.

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?? Thanx. -- gmx-users mailing listgmx-users@gromacs.org http://lists.

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

[gmx-users] fatal error occuring.

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?? Thanx. ---

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

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

Hi all, I'm getting errors in MPI_Allreduce what I restart an REMD simulation. It has occurred every time I have attempted an REMD restart. I'm posting here to check there's not something obviously wrong with the way I'm doing the restart which is causing it. I restart an REMD run using: --

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

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

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 = 1 nstxout = 0 nstxtcout

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

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

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 the environment variable GMX_MAXCONSTRWARN to -1

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

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

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 select=2:ncpus=8:mpiprocs=8 #PBS -l walltime=024:00:00 cd $P

[gmx-users] fatal error

Hi all Why is pull geometry direction not supported in g_wham ? I got the following error. I did this to compare with the same simulations but with pull geometry = distance. Fatal error: Pull geometry direction not supported -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromac

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

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

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_list/namd-l/14046.

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)

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

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) What is the error about?

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

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