Re: [gmx-users] Making group of different atoms

you can just manually make the index file as Sohaib > suggested. An index group is just: > > [ name_of_group ] > ;atomnr of atoms that make up the group eg. > 1566 1567 1569 1571 1574 1579 etc.. > > On 12 July 2018 at 16:24, Chetan Puri wrote: > > > Yes, I have t

Re: [gmx-users] Making group of different atoms

Yes, I have tried but I am having trouble in making a group for atoms with different numbers. On Wed, 11 Jul 2018, 22:29 Quyen V. Vu, wrote: > Have you try make_ndx tool of Gromacs? > > On Wed, Jul 11, 2018, 00:09 Chetan Puri wrote: > > > Can someone guide me in how to make

[gmx-users] Making group of different atoms

Can someone guide me in how to make a group for atoms number 1566, 1567, 1569,1571,1574&1579, which all belong to a tyrosine residue number 128 of protein. Since I need to measure distance between two groups (ligand and protein) Regards, Chetan -- Gromacs Users mailing list * Please search

Re: [gmx-users] Permeability determination

n the lipids, you perturb their dynamics and likely influence the free energy of permeation across the membrane " So can you please explain in more simple way . CHETAN On 11/14/17 9:32 AM, Chetan Puri wrote: > I am trying to do umbrella sampling for a ligand and dopc membrane. > For

[gmx-users] Permeability determination

I am trying to do umbrella sampling for a ligand and dopc membrane. For umbrella sampling pulling step, I am unable to posre_restrain the lipid, since grompp gives a error due to conflict between posre_restrain file of lipid and itp file of lipid. I have 128dopc molecules. So can someone suggest

Re: [gmx-users] Determining a ligands permeability

Thanks for the reply, But I could not understand what you want to say, Since I am trying to do the ligand and membrane simulation while constraining the lipid CHETAN On 6 Nov 2017 5:24 pm, "Justin Lemkul" wrote: > > > On 11/6/17 12:22 AM, Du, Yu wrote: > >> Hi, Justin, >> >>

[gmx-users] Determining a ligands permeability

I have tried to do an umbrella sampling for a ligand (drug) and membrane as per the gromacs tutorial. Now i want to calculate permeability and diffusibility for this ligand, so can anyone suggest how to proceed further. Since there is some literature available but it does not show the proper

[gmx-users] Drug membrane simulation

I want to determine permeability of drug molecules through various lipid membranes. Building the membrane i am able to do with the kalp-dppc tutorial, but for placing the drug molecule above the membrane i am not getting proper solution. So can someone suggest how to place the drug molecule above

[gmx-users] Gromacs 5.1.4

I am trying to install Gromacs 5.1.4 on centos7 with gpu Tesla k40 But on the make step I am getting error nvcc fatal : unsupported gpu architecture 'compute_20' So can anyone suggest how to resolve it. CHETAN -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Polymer topology file

Is there any example or tutorial for building a polymer topology/itp file. I need for PVP. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Exporting md frames to pdb format

Thanks for the reply On 26 Apr 2017 8:53 pm, "Justin Lemkul" <jalem...@vt.edu> wrote: > > > On 4/26/17 11:21 AM, Chetan Puri wrote: > >> I want to determine if new pockets are developed during md simulation of a >> protein using fpocket. >> So is th

[gmx-users] Exporting md frames to pdb format

I want to determine if new pockets are developed during md simulation of a protein using fpocket. So is there any way we can convert the trajectory file to individual pdb files or is there any way we can do it in Gromacs -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Protein-ligand opls ff

I want to use Desmond out.cms file for gromacs, as I want to compare MD output from Desmond and gromacs . Since Desmond uses OPLS, I will also be needing OPLS in Gromacs On 24 Feb 2017 12:11 am, "Justin Lemkul" <jalem...@vt.edu> wrote: > > > On 2/23/17 10:53 AM, Chetan Pu

Re: [gmx-users] Protein-ligand opls ff

I have few questions 1) I tried topolgen script but it doesn't assign proper atoms, so if I change the atom type, what will happen to bonds and angles 2) can we use Desmond output for gromacs directly On 22 Feb 2017 7:29 am, "Chetan Puri" <chetanpu...@gmail.com> wrote: >

Re: [gmx-users] Protein-ligand opls ff

I am from Organic chemistry background and I don't know much about inorganic chemistry calculations. So I would request you if you could guide me , how to generate a topology file for a small molecule. e.g. ATP or benzoic acid for OPLS ff On 21 Feb 2017 11:34 pm, "Justin Lemkul"

Re: [gmx-users] Ligand hybridization

aromatic ring is supposed to be after passing through prodrg. On 5 Jul 2016 10:26 pm, "Justin Lemkul" <jalem...@vt.edu> wrote: > > > On 7/5/16 10:50 AM, Chetan Puri wrote: > >> I am trying to do a protein- ligand simulation. >> >> And the prodrg server provi

[gmx-users] Ligand hybridization

I am trying to do a protein- ligand simulation. And the prodrg server provides the ligand out put by completely removing the double bonds(making it saturated) So is there any way to do it. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] charge calculations and topology

Can somebody suggest what could be the best possible way for generating small molecules topology file and charge determination ( OPLS force field) as I want carry out a simulation for miscell formation between small ligands. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] ligand topology & charge calculations

Can somebody suggest what could be the best possible way for generating small molecules topology file and charge determination ( OPLS force field) as I want carry out a simulation for miscell formation between small ligands. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] maestro cms file to gromacs

Is there any way to use maestro cms file for md simulations in gromacs. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe

Re: [gmx-users] miscelle formation using ligands only

of various molecules and use it . On Wed, Sep 16, 2015 at 5:20 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/15/15 11:01 PM, Chetan Puri wrote: > >> so what is the best option for topologies. >> >> > A force field you trust in concert with molecules tha

Re: [gmx-users] miscelle formation using ligands only

so what is the best option for topologies. On Wed, Sep 16, 2015 at 2:19 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/15/15 11:35 AM, Chetan Puri wrote: > >> thanks for you help and today i was able to solve the problem, >> actually my pdb file was made

Re: [gmx-users] miscelle formation using ligands only

; On 9/14/15 11:18 AM, Chetan Puri wrote: > >> i tried to prepare a topolgy file for my ligands and it contained >> following >> things, >> #include "gromos43a1.ff/forcefield.itp" >> #include "drg1.itp" >> #include"drg2.itp" >>

Re: [gmx-users] miscelle formation using ligands only

nt representation . so can you please help me out with this thing and also is there any other way by using gromacs and packing a system of different ligands (gromacs version 5.0.4) On Sun, Sep 13, 2015 at 6:43 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/13/15 3:47 AM,

Re: [gmx-users] miscelle formation using ligands only

a topology with oplsa.ff and include drug.itp files in that topology file. On Sunday, September 13, 2015, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/11/15 11:59 PM, Chetan Puri wrote: >> >> I am using gromacs for the first time . I have installed gromacs 5.0.4 >

[gmx-users] miscelle formation using ligands only

I am using gromacs for the first time . I have installed gromacs 5.0.4 version and i want to check a miscelle is formed or not using 5 different ligands in different ratios. I have gone through all basic tutorials on how to use gromacs ( lysosyme,protein-ligand). But i am stuck with the problem