[gmx-users] NME ACE

Raghunadha Reddy Burri burri at heineken.chemie.uni-dortmund.de
Tue Nov 11 19:57:01 CET 2003

Dear David,
Thanks for your suggestions,
I got .gro and .top files from your suggestions, 

pdb2gmx -f -ignh -ter pep2.pdb

working very nice
Thank you very much


Content-Description=embedded message
Subject: Re: [gmx-users] NME ACE
From: David van der Spoel <spoel at xray.bmc.uu.se>
To: gmx-users at gromacs.org
Date: 11 Nov 2003 16:24:27 +0100
Reply-To: gmx-users at gromacs.org

On Tue, 2003-11-11 at 16:17, Raghunadha Reddy Burri wrote:
> Dear David and GMX users,
> I have problem in pdb2gmx, please help me, this problem same as Peter Nagy
> your solved In July 8th 2003.
> As per your previous ( Peter Nagy) suggestions I was Changed
> NME --> NAC,
> CH3 --> CA
> but I am getting another error like
> Fatal error: atom N not found in residue 1ACE while combining tdb and rtp
you have to add the -ter option to pdb2gmx for interactive selection of
termini, then select none By default pdb2gmx adds NH3+ and COO- to your

> (details below)
> I dont want them to be protonated at two N-termini but for testing I was
> replaced with N in place 1HH3 (!!!) that opens another error like
> Fatal error: Residue 'CE' not found in residue topology database
> I am looking forward for suggestions to overcome this problem
> Thank you very much
> Raghu

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