[gmx-users] pdb2gmx error

Tawhid Ezaz ezaztaw at yahoo.com
Tue Nov 27 03:36:54 CET 2007

Thanks a lot Justin. It worked really nice. 

now I am stuck with another problem. I need to add the Building block GTP and GDP in 43a1, as I need to get the topology of a tubulin monomer.  I got the file from a old post here. 


I copied and pasted it into my file, yet, as the structure doesn't match it gave several errors. 

is there any way to  fix this?

Thanks a lot for your help. 


----- Original Message ----
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Monday, November 26, 2007 7:14:43 PM
Subject: Re: [gmx-users] pdb2gmx error

Quoting Tawhid Ezaz <ezaztaw at yahoo.com>:

> Hi,
> I have just started to learn gromacs. I am facing a problem to make
> file of a myoglobin. I got the pdb file from the csc tutorial.
> When i am running the pdb2gmx with
> pdb2gmx -f conf.pdb -p topol.top
> i get the message, HEME148 CAB1428   0.569
>  HEME148 CAC1437   0.562   0.820
> N-terminus: NH3+
> C-terminus: COO-
> Now there are 148 residues with 1451 atoms
> -------------------------------------------------------
> Program pdb2gmx, VERSION 3.3.1
> Source code file: pdb2top.c, line: 570
> Fatal error:
> atom N not found in residue 1ACE while combining tdb and rtp
> -------------------------------------------------------
> I was using 43a1 force field (0), {but none of them works}.
> i read some previous post and got the idea that there should be a N
 atom with
> should be linked with ACE, but my conf.pdb files does not have any. I
> topol.top file from the tutorial but didn't show how I can generate

Use the -ter option with pdb2gmx, and select 'none' when prompted.
  That way,
pdb2gmx does not look for an N-terminal nitrogen (which is obviously
 absent in
an acetyl group).


> I am a totally newbie, thus I am wondering what should I do. Which
 file I
> should correct to get rid of those? Do I need to know the bonding of
> atom in the molecule for that?
> Thanks in advance
> Tawhid


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080

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