Re: [gmx-users] question about g_sas: dgSolv

On 8/31/15 10:29 AM, ANTHONY C MANSON wrote: Hello: In the tool g_sas, what are the units of the dgSolv value that is output. The plot in which they occur says that the units are nm squared (seems strange to me). If this is true, how can one convert (ie. what is the conversion factor?) the

Re: [gmx-users] Free energy calculation using inter-molecular bonded interaction

On 8/31/15 11:20 AM, Atsutoshi Okabe wrote: Hi all, I have a question about how to use inter-molecular bonded interaction tool in GROMACS 5.1. I want to calculate binding free energy between protein and ligand adding harmonic restraint force to prevent the ligand from leaving the binding

Re: [gmx-users] computation of energy for energygrps + problem using g_enemat

On 8/31/15 10:33 AM, ANTHONY C MANSON wrote: Hello: energy for energygrps:I am trying to estimate the polar solvation energy of a 76 residueprotein at standard conditions. I am using the gromacs 4.5.3 dp release. I have set up a simulation with the solvated (using spce water) protein.I have

Re: [gmx-users] No such moleculetype DPPE

On 8/31/15 1:00 PM, Poncho Arvayo Zatarain wrote: Hello: i'm working in a simulation for a DPPC/DPPE membrane and when i use the instruction grompp -f minim.mdp -c dppc-dppe128.pdb -p topol_dppc.top -o em.tp for enrgy minimization, the following error appears: Fatal error: No such

Re: [gmx-users] extend a simulation just with xtc file

On 8/31/15 11:52 AM, Adriana Garro wrote: Dear Gromacs users, My 100 ns simulation finish but in a wrong way, I knew it when I tried to use an analizing tool and the message was the next one Fatal error: Magic Number Error in XTC file (read 0, should be 1995) It seems that this kind of

[gmx-users] structure changed after energy minimization

hi gmx users,i want to simulate prion protein(beta-sheets structure; model in modeller), but after minimization the structure totally changes into elongated form.what am i missing? i am doing implicit solvent simulation. this is the mdp file for minimization:  title               =cpp          

Re: [gmx-users] Impact of ignoring hydrogens

Dear Suniba, Matej is correct, but doing that can be quite tiresome. Easier I believe to just map the unrecognized names in the arn file ($GMXDATA/top/ffname/aminoacids.arn Atom renaming database Force fields often use atom names that do not follow IUPAC or PDB convention. The .arn database

Re: [gmx-users] HREX simulation

Dear Prof. Shirts, Prof. Abraham, Thanks so much for the detailed explanation. Sorry for the delay in responding, I didn't see the replies till now! I did increase the number of replicas, hope to see better results. have a great day, Shyno On Thu, Aug 27, 2015 at 12:35 PM, Shyno Mathew

Re: [gmx-users] Impact of ignoring hydrogens

Allright. I will try this option. Thank You very much for quick reply. Sent from my iPhone > On 31-Aug-2015, at 8:22 pm, Peter Stern wrote: > > Dear Suniba, > > Matej is correct, but doing that can be quite tiresome. Easier I believe to > just map the

[gmx-users] question about g_sas: dgSolv

Hello: In the tool g_sas, what are the units of the dgSolv value that is output. The plot in which they occur says that the units are nm squared (seems strange to me). If this is true, how can one convert (ie. what is the conversion factor?) the values to KJ/mol, or is this already done

[gmx-users] computation of energy for energygrps + problem using g_enemat

Hello: energy for energygrps:I am trying to estimate the polar solvation energy of a 76 residueprotein at standard conditions. I am using the gromacs 4.5.3 dp release. I have set up a simulation with the solvated (using spce water) protein.I have defined two energygrps: Protein SOL in the *.mdp

[gmx-users] Free energy calculation using inter-molecular bonded interaction

Hi all, I have a question about how to use inter-molecular bonded interaction tool in GROMACS 5.1. I want to calculate binding free energy between protein and ligand adding harmonic restraint force to prevent the ligand from leaving the binding site when the native ligand-receptor interaction

Re: [gmx-users] Calculation of Cv

No sir.i want to know whether it is possible to obtain from energies and enthalpy obtained from g_energy? On 31 Aug 2015 19:57, "David van der Spoel" wrote: > On 31/08/15 14:15, Sunil Ghimire wrote: > >> Dear sir, >> Thanks for suggestion.This is the theoritical

[gmx-users] extend a simulation just with xtc file

Dear Gromacs users, My 100 ns simulation finish but in a wrong way, I knew it when I tried to use an analizing tool and the message was the next one Fatal error: Magic Number Error in XTC file (read 0, should be 1995) It seems that this kind of error is related to the network file system. My

Re: [gmx-users] Calculation of Cv

2015-08-31 12:43 GMT-03:00 Sunil Ghimire : > No sir.i want to know whether it is possible to obtain from energies and > enthalpy obtained from g_energy? > The answer was just one google away: http://manual.gromacs.org/programs/gmx-energy.html Still, read about Heat

[gmx-users] No such moleculetype DPPE

Hello: i'm working in a simulation for a DPPC/DPPE membrane and when i use the instruction grompp -f minim.mdp -c dppc-dppe128.pdb -p topol_dppc.top -o em.tp for enrgy minimization, the following error appears: Fatal error: No such moleculetype DPPE, so it appears some warnings like: File

Re: [gmx-users] Fatal error: No molecule were defined in the system

This is only the include topology, but the functional topology for grompp needs a few more lines. Make another file such as below and this should run fine through grompp, provided you have a big enough box defined in 5-fu.gro. Note that this will run the 5-FU dynamics in the gas phase, since there

Re: [gmx-users] Split Trajectory file into parts

On 29/08/15 16:22, Justin Lemkul wrote: > > > On 8/29/15 9:10 AM, Johnny Lu wrote: >> Dear Users, >> >> Simulation writes to a Lustre file system (a distributed file system >> made >> of many hard drives). >> About 100 Gb was written in 1 hrs. After a while, gromacs 5.1 says it >> can't >> write

Re: [gmx-users] vaccume simulation

On 8/31/15 7:01 AM, tasneem kausar wrote: Dear gmx-users I am trying to calculate rmsd for protein backbone. I have done simulation in vacuum. There are for negative charges in the system. During solvation via genbox, 4 water molecule were added using -maxsol. The charges have been neutralized

Re: [gmx-users] mdrun error

On 8/31/15 12:41 AM, tasneem kausar wrote: Hi, I am trying to run final MD. The job terminated with the following error message. Fatal error: The initial cell size (0.875477) is smaller than the cell size limit (0.876000), change options -dd, -rdd or -rcon, see the log file for details

[gmx-users] Fatal error: No molecule were defined in the system

Dear all, hi, I'm simulating the drug "5-Flouorouracil", since its topology file is not available, I've written it by hand. But I got the error "No molecule were defined in the system" when run grompp. where could be the problem? Thank you in advance. Regards, Mehrnoosh The .itp file is

[gmx-users] vaccume simulation

Dear gmx-users I am trying to calculate rmsd for protein backbone. I have done simulation in vacuum. There are for negative charges in the system. During solvation via genbox, 4 water molecule were added using -maxsol. The charges have been neutralized by addition of 4 Na ion and water molecules

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

On 8/31/15 1:31 AM, Raag Saluja wrote: Yes,I did, Mark. Thanks! But I don't need GTP. The pdb file just shows a GTP-binding site. Can I get rid of this somehow? Or else, how may I get the .pdb file for GTP? Your .pdb file also contains GTP, if pdb2gmx is complaining about it. If it's not

Re: [gmx-users] Calculation of Cv

On 8/30/15 10:41 PM, Sunil Ghimire wrote: Dear sir, How can we calculate the value of Cv for noble gases? http://hyperphysics.phy-astr.gsu.edu/hbase/kinetic/shegas.html -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA

Re: [gmx-users] Fwd: NO BONDS IN TOPOLOGY FILES

On 8/31/15 4:03 AM, Alex Cullen wrote: Dear gmx-users, I am simulating a polymer, and I am really beginner in this area. when I execute pdb2gmx command I get posre.itp, topol.top, and conf.gro files, but there are no bonded, angles, and dihedral interactions in the topology file, only atoms

[gmx-users] topology making by ATB/PRODRG

Dear GMX users i d simulated a drug on a protein and in *ions.tpr* production process, i ve got below error: *Fatal error:number of coordinates in coordinate file (sol.gro, 29108) does not match topology (topol.top, 29116)* i know ATB server is useful for molecules at most 40

Re: [gmx-users] extend a simulation just with xtc file

:-( ok Thanks, I will have to run this simulation again. Bye Adriana *** Dra. Adriana D. Garro Química Medicinal Facultad de Química, Bioquímica y Farmacia Universidad Nacional de San Luis IMASL-CONICET San Luis, Argentina

Re: [gmx-users] Calculation of Cv

On 31/08/15 14:15, Sunil Ghimire wrote: Dear sir, Thanks for suggestion.This is the theoritical approach.I want to known how can we obtain Cv from the production run done with NVT ensemble? Is it possible to obtain from g_energy ? Have you tried? On 31 Aug 2015 17:18, "Justin Lemkul"

[gmx-users] Impact of ignoring hydrogens

Hello All I am doing protein ligand MD to view the interactions and effect of ligand on protein structure. However the NMR structure of protein encountered some warnings and considering that, i ignored hydrogens by -ignh. I believe that the hydrogen bonding might reduce due to this action. Is

Re: [gmx-users] Impact of ignoring hydrogens

Dear Suniba, The -ignh flag of pdm2gmx removes all the hydrogens from the pdb file and then adds them according to simple geometric rules. This should be fine for most hydrogens except for the exchangable protons of acidic and basic residues, where the algorithm quite possibly will not protonate