[gmx-users] merging and renumbering topology atoms
stu_psyc at nimhans.kar.nic.in
Mon Oct 27 15:09:01 CET 2003
Even I had the same problem when doing simulations with non-bio
molecules. Instead of getting the information from PRODRG, you can
calculate the charges,bond angle,and bond lengths by using "gamess" or
any other software or can be done manually. Then give all those
informations in gromacs topology file by manuplating ffgmx.rtp and
ffgmxbon.itp files. it worked out for us.
All the best
Blaise M Costa
"The more we learn the more we realize how little we know." -
Department of Psychopharmacology,
National Institute of Mental Health And Neuro Sciences (NIMHANS),
India. Tel: 91 80 6995112.
From: <christoph.nimptsch at uni-tuebingen.de>
To: <gmx-users at gromacs.org>
Date: Mon, 27 Oct 2003 12:25:00 -0000
Subject: [gmx-users] merging and renumbering topology atoms
> I created a ligand with PRODRG and now I want to define distance
> As far as I know gromacs expects all atoms in one file.
> So, my idea was to renumber the atoms in the topology DRGGMX.ITP and
> it in protein.top.
> Is there any programm, that can do the renumbering? Or is there a
> switch in
> PRODRG, which forces the atoms to be numbered from a certain number?
> Thanks in advance,
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> gmx-users at gromacs.org
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