Re: [gmx-users] Residue 'DEF' not found in residue topology database

Hi Justin, Thank you for your reply. Before I contacted you and do what you suggested , I did the following way: 1) Firstly, I created the lipopetide (12 Carbon atoms (tail) + Val-Val-Ala-Gly-Glu-Arg-Gly-Asp) using ChemDraw and saved as a PDB. 2) Then, I pasted my pdb file to the The

[gmx-users] Minimisation restraints

Hi everyone, please I don't have access to the mailing list, (there must be a problem in the archive) and I need to know if there's a way of doing energy minimisation with restraints on the backbone. In other words, I want to minimize the sidechaines in my protein without moving (or minimizing)

[gmx-users] 9 particles communicated to PME node 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.

Respected Sir, Myself Haresh Ajani from National Institute of Pharmaceutical Education Research. I am using gromacs version 4.5.3. I am working on molded Protein. I am facing one problem in gromacs after minimization of the protein. I have put my query here. Fatal Error :

[gmx-users] negative steps from tpbconv

Hi, I am trying to extend the run time in tpr file to include more steps using tpbconv… This has worked well for a while, but now I get two errors… One is that it writes “now -207466 steps”, which doesn’t make sense – why is this number negative… Also, “You've simulated long enough.

Re: [gmx-users] negative steps from tpbconv

Hi Jesper, This occurs when you ask for a number of steps that exceed the the size of an integer! I got the same problem recently ... The only solution I found was to make a new mdp file where t0 is the old time and asking for the extension you need ... you can give trr and edr files to grompp

[gmx-users] topology files for ligands in MD Simulation under OPLS AA force field

Dear All: I am using GROMACS package to do molecular dynamics simulations under OPLS_AA force field. I encounter some problems when preparing the topology files of small molecules (ligands).My questions are as follows: 1, how to chose the atom type of each atom from the ligands? 2, how to

Re: [gmx-users] Residue 'DEF' not found in residue topology database

Emine Deniz Tekin wrote: Hi Justin, Thank you for your reply. Before I contacted you and do what you suggested , I did the following way: 1) Firstly, I created the lipopetide (12 Carbon atoms (tail) + Val-Val-Ala-Gly-Glu-Arg-Gly-Asp) using ChemDraw and saved as a PDB. 2)

Re: [gmx-users] Minimisation restraints

Carla Jamous wrote: Hi everyone, please I don't have access to the mailing list, (there must be a problem in the archive) and I need to know if there's a way of doing energy minimisation with restraints on the backbone. In other words, I want to minimize the sidechaines in my protein

Re: [gmx-users] 9 particles communicated to PME node 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.

ajani haresh wrote: Respected Sir, Myself Haresh Ajani from National Institute of Pharmaceutical Education Research. I am using gromacs version 4.5.3. I am working on molded Protein. I am facing one problem in gromacs after minimization of the protein. I have

Re: [gmx-users] topology files for ligands in MD Simulation under OPLS AA force field

mirc...@sjtu.edu.cn wrote: Dear All: I am using GROMACS package to do molecular dynamics simulations under OPLS_AA force field. I encounter some problems when preparing the topology files of small molecules (ligands).My questions are as follows: 1, how to chose the atom type of each atom

RE: [gmx-users] negative steps from tpbconv

Hi Xavier, That worked, thanks… Would it also work if I just gave the old state.cpt file to mdrun? Jesper From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of XAvier Periole Sent: 24. februar 2011 12:19 To: Discussion list for GROMACS users Subject:

Re: [gmx-users] negative steps from tpbconv

Hi Jesper, Using a .cpt file will also work with the modified .tpr file. Maybe it is also worth considering using the -maxh option to mdrun, with nsteps in the .mdp file set to -1 (run infinitely). That avoids the hassle with extensions. Cheers, Tsjerk 2011/2/24 Jesper Sørensen li...@jsx.dk:

[gmx-users] How to countting hydrogen bond lifetime and donor--acceptor residue's atom ?

Dear all I want to count all of the hydrogen bond's lifetime and donor-acceptor atoms in simulation,but I don't know how to do it. In many papers,the hydrogen bonds are list in this form: Donor Acceptor %Exist. ARG58

Re: [gmx-users] How to countting hydrogen bond lifetime and donor--acceptor residue's atom ?

For now, use the kinetic model by Luzar and Chandler which is implemented in Gromacs. There's an implementation of the Geminate recombination model by Omer Markovitch underway, but it still has convergence problems that needs to be dealt with. Erik gromacs564 skrev 2011-02-24 13.11: Dear

[gmx-users] CNT topology

Dear All Users   I am beginner to GROMACS. I want to simulate CNT in water. I made pdb file by VMD and then made .gro by editconf -f file.pdb -o file.gro -box 4 command. then for made topology file, I use .n2t itp, .itp, .rtp, ff.dat, and by x2top -f file.gro -o topol.top -ff cnt_oplsaa -name

Re: [gmx-users] How to countting hydrogen bond lifetime and donor--acceptor residue's atom ?

Maybe I misunderstood. What you presented in a table is the hbond occupancies, not the lifetimes. I beleve that Justin Lemkul once posted a script for calculating occupancies. Erik Erik Marklund skrev 2011-02-24 13.15: For now, use the kinetic model by Luzar and Chandler which is implemented

Re: [gmx-users] CNT topology

sara wrote: Dear All Users I am beginner to GROMACS. I want to simulate CNT in water. I made pdb file by VMD and then made .gro by editconf -f file.pdb -o file.gro -box 4 command. then for made topology file, I use .n2t itp, .itp, .rtp, ff.dat, and by x2top -f file.gro -o topol.top -ff

Re: [gmx-users] How to countting hydrogen bond lifetime and donor--acceptor residue's atom ?

Erik Marklund wrote: Maybe I misunderstood. What you presented in a table is the hbond occupancies, not the lifetimes. I beleve that Justin Lemkul once posted a script for calculating occupancies. The posted output is from my script, and it is indeed a simple percentage of times in which

Re: [gmx-users] negative steps from tpbconv

I am not sure the use of cpt would work! I might have tried and got a problem since the cpt might define where it is going (nsteps) ... to be tried! @Tsjerk: I have not been able to use the nsteps set to -1 for some reason it was telling it had ran enough! Any idea why would that be? On Feb

RE: [gmx-users] negative steps from tpbconv

Using the cpt file didn't work for me - it remembered the nsteps and quit before even running anything. Without getting into the details, I am changing the temperature along the way in my simulation and therefore I can't use nsteps -1 either. But Xavier's first suggestion worked, so I will

Re: [gmx-users] negative steps from tpbconv

Hi, The .cpt defines the state, not the number of steps to go for. Setting nsteps to -1 should work for the new (4.5 definitely, 4.0 I'm not sure) versions of gromacs. I think it was introduced right after the -maxh option was. @Xavier: I added a number of editing options to tpbconv (4.5.1),

[gmx-users] How to countting Hbonds lifetime

Hi Erik and Justin Thanks for your reply. I want to obtain the HBond's permanence time.May be it's occupancies that you said. So,could you send me the script? Thank you very much. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] g_rms and g_cluster

Dear All I want to calculate RMSD of one side chain residue from simulation trajectory after full backbone alignment as well as translating to coincide CA of the residue of interest. Is it possible to do with g_rms both backbone alignment as well as translating to coincide CA. Another

Re: [gmx-users] g_rms and g_cluster

shahid nayeem wrote: Dear All I want to calculate RMSD of one side chain residue from simulation trajectory after full backbone alignment as well as translating to coincide CA of the residue of interest. Is it possible to do with g_rms both backbone alignment as well as translating to

Re: [gmx-users] How to countting Hbonds lifetime

gromacs564 wrote: Hi Erik and Justin Thanks for your reply. I want to obtain the HBond's permanence time.May be it's occupancies that you said. So,could you send me the script? The output you posted before suggested you were using my script for occupancy. Is this not the case?

[gmx-users] PMF from pull code, unexpected results

Michael: your mdp options indicated using US and my stance is that, using US, you are incorrect to say that And you will get the SAME result if you do this calculation in one or in three dimensions (pulldim NNY or pulldim YYY). Nevertheless, I'm a little perturbed by your call out for help

[gmx-users] %exist hydrogen bond - difference between number of lines in input and output files

Dear Justin I have a question about output file (summary_HBmap.dat). my input file (hbound.ndx) is as follows: [ hbonds_Protein-ab_interfacial ] 1019 1021 13088 1019 1021 23621 1016 1018 23621 1013 1014 12392 1013 1014 23621 992994 12392 946949

Re: [gmx-users] %exist hydrogen bond - difference between number of lines in input and output files

leila karami wrote: Dear Justin I have a question about output file (summary_HBmap.dat). my input file (hbound.ndx) is as follows: [ hbonds_Protein-ab_interfacial ] 1019 1021 13088 1019 1021 23621 1016 1018 23621 1013 1014 12392 1013 1014 23621 992994

[gmx-users] Re: How to countting Hbonds lifetime

Hi Justin What is your means that the HBond's occupancy ? Can you tell me the difference about Hbonds lifetime and occupancy? I want to know which residues form the Hbond and the donor-acceptor atoms. The g_hbond can do it? Thank you very much. -- gmx-users mailing list

Re: [gmx-users] Re: How to countting Hbonds lifetime

gromacs564 wrote: Hi Justin What is your means that the HBond's occupancy ? Can you tell me the difference about Hbonds lifetime and occupancy? The script I wrote simply counts the number of times a certain hydrogen bond appears in the output that g_hbond already gives you and

[gmx-users] water-medited hydrogen bonds - %exist hydrogen bonds

Dear Justin very thanks for your reply. I used for script two times: 1) between proten and interfacial waters. 2) between dna and same water molecules. using what I said above, can I obtain what water molecules form water-mediated hydrogen bond between protein and dna? if my way is wrong,

[gmx-users] PMF from pull code, unexpected results

Michael: your mdp options indicated using US and my stance is that,using US, you are incorrect to say that And you will get the SAMEresult if you do this calculation in one or in three dimensions(pulldim NNY or pulldim YYY). this has nothing to do with the mdp file ... i was

[gmx-users] topology files for ligands in MD Simulation under OPLS AA force field

mircial at sjtu.edu.cn mircial at sjtu.edu.cn wrote I am using GROMACS package to do molecular dynamics simulations under OPLS_AA force field. I encounter some problems when preparing the topology files of small molecules (ligands).My questions are as follows: 1, how to chose the atom type

Re: [gmx-users] Minimisation restraints

Have a look at side-chain optimization programs like SCWRL4 ( http://dunbrack.fccc.edu/scwrl4/index.php). If this is what you are looking for then running SCRWL4 will be much easier than setting up your one restraints in GROMACS. Thomas On 24 February 2011 12:31, Carla Jamous

[gmx-users] GAUSSIAN Error message

Hello, I am getting an unknown error message in the submission of the G03 file: QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE. # HF/6-31G OPT FREQ ^M ^M ARGUSLAB-GENERAT ' Last state=GCL TCursr= 909 LCursr= 20 Error termination via Lnk1e in

Re: [gmx-users] GAUSSIAN Error message

On February 24, 2011 at 10:29 AM Sergio Manzetti sergio.manze...@vestforsk.no wrote: Hello, I am getting an unknown error message in the submission of the G03 file: QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE.

Re: [gmx-users] GAUSSIAN Error message

No. It contains a charged Gandolinium ion in the middle of a buckyball. On Fri, Feb 25, 2011 at 2:59 AM, TJ Mustard musta...@onid.orst.edu wrote: On February 24, 2011 at 10:29 AM Sergio Manzetti sergio.manze...@vestforsk.no wrote: Hello, I am getting an unknown error message in the

[gmx-users] Re: gmx-users Digest, Vol 82, Issue 189

attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110224/34350756/attachment-0001.html -- Message: 3 Date: Fri, 25 Feb 2011 03:07:07 +0800 From: Sergio Manzetti sergio.manze...@vestforsk.no Subject: Re: [gmx-users] GAUSSIAN

[gmx-users] g_dipole

Hello, I am calculating dipole autocorrelation function for my system. I run the simulation for 500ps and the plot of dipole autocorrelation function shows the results for 250 ps. I used the following command g_dipoles -f water.trr -s water.tpr -c -corr total Can anyone tell whats the

Re: [gmx-users] g_dipole

Nilesh Dhumal wrote: Hello, I am calculating dipole autocorrelation function for my system. I run the simulation for 500ps and the plot of dipole autocorrelation function shows the results for 250 ps. I used the following command g_dipoles -f water.trr -s water.tpr -c -corr total Can

Re: [gmx-users] g_dipole

How can I make prog. to read all frames. On Thu, February 24, 2011 2:34 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, I am calculating dipole autocorrelation function for my system. I run the simulation for 500ps and the plot of dipole autocorrelation function shows the

Re: [gmx-users] g_dipole

Nilesh Dhumal wrote: How can I make prog. to read all frames. I already answered this. Use a proper setting for -acflen. -Justin On Thu, February 24, 2011 2:34 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, I am calculating dipole autocorrelation function for my system.

[gmx-users] henry constant

Hello, I want to calculate the henry constant for a soluble gas in a solvent. For that, I use the tool -fee in g_energy to get deltaG. Is that the excess chemical potential, with which I can claculate the henry constant? Regards, Thomas -- NEU: FreePhone - kostenlos mobil telefonieren und

[gmx-users] Stress/strain analysis

Dears, Can anyone explain to me if we can run a stress/strain analysis with Gromacs and if yes, how. Many thanks, Adama -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] g_dipole

the program actually reads all frames, but it computes the correlation up to half of the total length of the data (it is a homoscedasticity issue, you should read some textbook on time series analysis before you increase the output length using -acflen) best André On Thu, Feb 24, 2011 at 5:04

[gmx-users] em mdrun

Hello all, When I issue mdrun program for EM altough this is not a parallel simulation, 6 nodes are getting involved. I am using 4.5.3 and get the error: Reading file em-l0.5.tpr, VERSION 4.5.3 (single precision) Starting 16 threads Does anyone have idea why is this happening? Thanks --

Re: [gmx-users] em mdrun

Nick wrote: Hello all, When I issue mdrun program for EM altough this is not a parallel simulation, 6 nodes are getting involved. I am using 4.5.3 and get the error: Reading file em-l0.5.tpr, VERSION 4.5.3 (single precision) Starting 16 threads Does anyone have idea why is this

[gmx-users] Help please.

Hello all, I am an undergrad student and I am trying to learn how to run gromacs. My computer knowledge is somewhat limited so please have patience with me. I have been trying to run through the initial tutorial right now I am at the preprocessing of cpeptide with grompp and I keep getting an

RE: [gmx-users] Help please.

Best place to start is to provide an exact copy paste of the command you used, then an exact copy/paste of the error message. A good resource for errors is http://www.gromacs.org/Documentation/Errors and searching the emailing list http://www.gromacs.org/Support/Mailing_Lists/Search Catch

Re: [gmx-users] em mdrun

Hello Justin, I forgot to say that with 16 nodes I am getting message below. I search the list and used -pd option but it takes much much loner than one processor! --- Program mdrun, VERSION 4.5.3 Source code file: domdec.c, line: 6428 Fatal

Re: [gmx-users] em mdrun

Nick wrote: Hello Justin, I forgot to say that with 16 nodes I am getting message below. I search the list and used -pd option but it takes much much loner than one processor! Some systems just don't scale particularly well. ---

[gmx-users] index file groups

Hello to all, Please help me with the following questions. Your attention is greatly appreciated. 1- I have an inquiry about index groups. If I specify all my solute chains as a whole in one group [all chains] (including n chains having m atoms each) and calculate interaction energies between