[gmx-users] ATB and PRODRG

Dear gmx users I am using gromos96 54 a7 and gromos 96 a1 force fiels to simulate tow various complexes  ( protein + ligand). and  used ATB and PRODRG  to create topology files for them, respectively. I dont know anything about editing ATB and PRODRG' topology files but reassigingn their

Re: [gmx-users] ATB topology: itp to top conversion

Thank you Mark and Justin! That makes sense, of course!!! Many thanks. With best wishes Anna > On Jun 13, 2017, at 17:22, Mark Abraham wrote: > > Hi, > >> On Wed, Jun 14, 2017 at 1:07 AM Anna Lappala wrote: >> >> Dear all, >> >> I am

Re: [gmx-users] ATB topology: itp to top conversion

Hi, On Wed, Jun 14, 2017 at 1:07 AM Anna Lappala wrote: > Dear all, > > I am confused: I have my pdb file as well as the itp file produced by ATB. > I want to convert these into top and gro files but the molecule is not > recognised by the forcefield when I do the

Re: [gmx-users] ATB topology: itp to top conversion

On 6/13/17 7:06 PM, Anna Lappala wrote: Dear all, I am confused: I have my pdb file as well as the itp file produced by ATB. I want to convert these into top and gro files but the molecule is not recognised by the forcefield when I do the following: pdb2gmx -f input.pdb -o output.gro -i

[gmx-users] ATB topology: itp to top conversion

Dear all, I am confused: I have my pdb file as well as the itp file produced by ATB. I want to convert these into top and gro files but the molecule is not recognised by the forcefield when I do the following: pdb2gmx -f input.pdb -o output.gro -i topology.itp I have looked through tutorials

[gmx-users] ATB parametrization of small molecule

Hello everyone I want to simulate a protein ligand docked complex using GROMOS96 43a1 force field. I have prepared the ligand topology using ATB server. However, I want to know how can I validate the results of ATB when no experimental or computational data is available for small molecule. I have

Re: [gmx-users] ATB server (charge assign)

On 7/11/16 2:14 AM, elham tazikeh wrote: Dear Justin thanks for your good advise as you're mentioned, i must include necessary file next to other force field files in my directory my version of gromaces is 4.6.5, and my force field is gromos 53a6 1-concerning below message, which ones is

[gmx-users] ATB server (charge assign)

Dear Justin thanks for your good advise as you're mentioned, i must include necessary file next to other force field files in my directory my version of gromaces is 4.6.5, and my force field is gromos 53a6 1-concerning below message, which ones is appropriate for me? Gromacs3.x.x-4.0.x 53a6-54a7

[gmx-users] ATB

Dear All Does the type of chemical bond (single, double, triple), built by JSME Molecular Editor, directly influence on the final results of Automated Topology Builder (http://compbio.biosci.uq.edu.au/atb/ ), not by number of built protons? I built a molecule with a some double bond, number of

Re: [gmx-users] ATB

On 4/1/15 8:30 AM, Vasiliy Znamenskiy wrote: Dear All Does the type of chemical bond (single, double, triple), built by JSME Molecular Editor, directly influence on the final results of Automated Topology Builder (http://compbio.biosci.uq.edu.au/atb/ ), not by number of built protons? I built

[gmx-users] ATB SERVER

hi my friends I use ATB server for my ligands. which are itp and pdb file used for ligands in md simulation by gromacs. thanks a lot -- 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

Re: [gmx-users] ATB SERVER

There are probably a few tutorials that describe what you're trying to do. Probably none of them are exactly right, but you will learn from doing them regardless. Please do a preliminary search for information before asking questions! :-) Mark On Dec 1, 2013 10:38 PM, Mahboobeh Eslami