[gmx-users] merging and renumbering topology atoms

Stud_Psychopharm stu_psyc at nimhans.kar.nic.in
Mon Oct 27 15:09:01 CET 2003

Dear christoph,
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." - 
R.Buckminster Fuller 

Blaise M.
Graduate Student,
Department of Psychopharmacology,
National Institute of Mental Health And Neuro Sciences (NIMHANS),
India. Tel: 91 80 6995112.

-----Original Message-----
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

> Hello,
> I created a ligand with PRODRG and now I want to define distance
> constraints.
> 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
> include
> 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,
> Christoph
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