[gmx-users] REGARDING PROTEIN LIGAND SIMULATION

Hi gromacs users, I am working on protein-ligand simulation..The commands were given in the following order (1) source leaprc.ff14SB loadAmberParams frcmod.tip4pew loadAmberParams frcmod.ionsjc_tip4pew source leaprc.gaff LIG = loadmol2 LIG.mol2 loadamberparams LIG.frcmod check LIG receptor =

Re: [gmx-users] MM dihedral scanning

I was thinking of a potential solution for this. Please let me know your opinion as expert. Sorry, if it seems stupid :-) I have the QM scan profile already. 1-4 interactions for this dihedral must be included in charmm36. My idea: I was thinking to find the dihedral parameters *purely

Re: [gmx-users] MM dihedral scanning

On 1/12/17 10:21 PM, Mohsen Ramezanpour wrote: On Thu, Jan 12, 2017 at 6:31 PM, Justin Lemkul wrote: On 1/12/17 7:47 PM, Mohsen Ramezanpour wrote: On Thu, Jan 12, 2017 at 4:24 PM, Justin Lemkul wrote: On 1/12/17 3:18 PM, Mohsen Ramezanpour wrote:

Re: [gmx-users] MM dihedral scanning

On Thu, Jan 12, 2017 at 4:24 PM, Justin Lemkul wrote: > > > On 1/12/17 3:18 PM, Mohsen Ramezanpour wrote: > >> Dear Gromacs users, >> >> For parameterization of a molecule in Charmm36, I have got the QM scanning >> and partial charges from GAMMP server. However, the fitted

Re: [gmx-users] MM dihedral scanning

On 1/12/17 7:47 PM, Mohsen Ramezanpour wrote: On Thu, Jan 12, 2017 at 4:24 PM, Justin Lemkul wrote: On 1/12/17 3:18 PM, Mohsen Ramezanpour wrote: Dear Gromacs users, For parameterization of a molecule in Charmm36, I have got the QM scanning and partial charges from

Re: [gmx-users] REGARDING PROTEIN LIGAND SIMULATION

On 1/12/17 10:02 PM, Subashini .K wrote: Hi gromacs users, I am working on protein-ligand simulation..The commands were given in the following order (1) source leaprc.ff14SB loadAmberParams frcmod.tip4pew loadAmberParams frcmod.ionsjc_tip4pew source leaprc.gaff LIG = loadmol2 LIG.mol2

Re: [gmx-users] MM dihedral scanning

On Thu, Jan 12, 2017 at 6:31 PM, Justin Lemkul wrote: > > > On 1/12/17 7:47 PM, Mohsen Ramezanpour wrote: > >> On Thu, Jan 12, 2017 at 4:24 PM, Justin Lemkul wrote: >> >> >>> >>> On 1/12/17 3:18 PM, Mohsen Ramezanpour wrote: >>> >>> Dear Gromacs users,

Re: [gmx-users] MM dihedral scanning

On 1/12/17 10:29 PM, Mohsen Ramezanpour wrote: I was thinking of a potential solution for this. Please let me know your opinion as expert. Sorry, if it seems stupid :-) I have the QM scan profile already. 1-4 interactions for this dihedral must be included in charmm36. My idea: I was

Re: [gmx-users] MM dihedral scanning

On Thu, Jan 12, 2017 at 8:36 PM, Justin Lemkul wrote: > > > On 1/12/17 10:21 PM, Mohsen Ramezanpour wrote: > >> On Thu, Jan 12, 2017 at 6:31 PM, Justin Lemkul wrote: >> >> >>> >>> On 1/12/17 7:47 PM, Mohsen Ramezanpour wrote: >>> >>> On Thu, Jan 12, 2017 at

[gmx-users] MM dihedral scanning

Dear Gromacs users, For parameterization of a molecule in Charmm36, I have got the QM scanning and partial charges from GAMMP server. However, the fitted parameters are not good enough. I decided to do the MM scanning and try to get better parameters for the dihedral. Unfortunately, I do not

[gmx-users] Fwd: Regarding gromacs

-- Forwarded message -- From: Dilip H N Date: Thu, Jan 12, 2017 at 11:40 AM Subject: Re: Regarding gromacs To: Mark Abraham Hello , While creating the topology fie from the perl interpreter, the topology file is created and

[gmx-users] Gromacs

Hello , While creating the topology fie from the perl interpreter, the topology file is created and a file selection_atoms_raw file is also created..?? hw is this possible..?? hope that is wrong. -- With Best Regards, DILIP.H.N Ph.D Student, Research Scholar, Department of Chemistry,

[gmx-users] Gromacs

i have a molecule of an acid... how can i create a topology file from that and do the simulation..?? i cant use gmx pdb2gmx -f file.pbd -o file.gro since it asks force feild , and thn water model..?? i dont want water to be added (since it is asking water model)... how can i proceed with my

[gmx-users] choosing group of atoms in trjconv

Hi, I’m trying to get coordinates of the Protein-H group from a .trr file with trjconv. I do the following: echo 2 | gmx trjconv -f all.trr -s nvt.tpr -o out.pdb Is there a way to get rid of the echo command and pass the information that I want the second group with a flag to trjconv,

[gmx-users] Results analysis of gromacs by VMD.

dear gromacs users,, i have done simulation by gromacs and now i want to analyse the results of it by VMD. when i open VMD for drawing RMSD trajectory tool..i dont get graph..and terminal gives me error..that is--ignoring plot..As the plot is not shown by it..i have attached the file and will hv

Re: [gmx-users] Results analysis of gromacs by VMD.

Hi, For help with VMD, please ask on their mailing list. They'll likely want more details on what you did and what the error message was. Mark On Thu, 12 Jan 2017 10:32 maria khan wrote: > dear gromacs users,, > > i have done simulation by gromacs and now i want to

Re: [gmx-users] choosing group of atoms in trjconv

Hi, No, that's the best you can do, except perhaps by naming the group, in case the order ever changes Mark On Thu, 12 Jan 2017 10:34 Irem Altan wrote: > Hi, > > I’m trying to get coordinates of the Protein-H group from a .trr file with > trjconv. I do the following: > >

[gmx-users] Running GROMACS in cluster with SGE

Hi all, I am trying to run a simulation on a cluster with SGE queue system with this script: *** #!/bin/bash #$ -cwd #$ -pe parallel 16 #number of cores #$ -q main.q #name of the queue #$ -q mai...@xbes23.akbester.zz #one can choose particular node #$ -e stderr.log # redirections for

Re: [gmx-users] domain decomposition error in the energy minimization step

Hi Qasim, > On 11 Jan 2017, at 20:29, Qasim Pars wrote: > > Dear Carsten, > > Thanks. The forward state simulations works properly with mdrun -ntmpi 8 > -ntomp 2 or mdrun -ntmpi 4 -ntomp 4 as you suggested. > For the backward state GROMACS still gives too many lincs

Re: [gmx-users] MM dihedral scanning

On 1/12/17 3:18 PM, Mohsen Ramezanpour wrote: Dear Gromacs users, For parameterization of a molecule in Charmm36, I have got the QM scanning and partial charges from GAMMP server. However, the fitted parameters are not good enough. That's very surprising. What's wrong with what GAAMP gave

Re: [gmx-users] domain decomposition error in the energy minimization step

Hi Carsten, I think I couldn't clearly explain the protocol that I follow. Sorry for that. Firstly, I do the EM, nvt (100 ps), npt (100 ps) and md (100 ns) steps for the equilibrium. In all those steps I use the below free energy parameters for the forward state: free-energy = yes init-lambda

Re: [gmx-users] ERROR IN GROMPP

On 1/12/17 8:19 AM, Subashini .K wrote: Hi gromacs users, I got an error when the following command gmx grompp -f em.mdp -c complex_GMX.gro -p complex_GMX.top -o em The corresponding em.mdp was ; to test ; grompp -f em.mdp -c test_GMX.gro -p test_GMX.top -o em.tpr -v ; mdrun -v -deffnm