[gmx-users] PLease it's very important......help needed

Rahul Karyappa r.karyappa at ncl.res.in
Thu Aug 25 14:26:16 CEST 2005

Dear Mark,

    Thank you for your kind reply. As you said I have
defined the residues in the .rtp file. When I ran grompp command it
gave me following error:

Fatal error: Bonded/nonbonded atom type 'C3' not found!

What may be the reason? Do I need to enter the residue some oher file?

Thanking you in advance. I am stuck please reply me for this.

Waiting for your kind reply.

-- Original Message --
From: "Marc F. Lensink" <lensink at scmbb.ulb.ac.be>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: Thu, 18 Aug 2005 11:51:27 +0200
Subject: Re: [gmx-users] problem while entering a new residue in ffgmx.rtp file
On Thu, Aug 18, 2005 at 03:09:04PM +0530, Rahul Karyappa wrote:
> Dear all,
>    I have a polyethylene.pdb file for 10 repeat units of
> polyethylene. I want to define atoms and bonds for residue PE in the
> ffgmx.rtp file. When I enter all the atoms as it is in the .pdb file
> and define the bonds, I am able to run pdb2gmx.  But  if I
> want to run pdb2gmx on higher no. of repeat units then
> it will be time-consuming to define each atom and bond. Can I add atoms
> and bonds for one repeat unit
you have to define 3 'residues' in the .rtp file:
* head
* section (the repeating unit)
* tail
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