Quoting Tawhid Ezaz <[EMAIL PROTECTED]>:
> Hi,
>
> I have just started to learn gromacs. I am facing a problem to make topology
> 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 have
> topol.top file from the tutorial but didn't show how I can generate that.
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).
-Justin
>
> 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 every
> atom in the molecule for that?
>
> Thanks in advance
>
> Tawhid
>
>
>
>
>
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
========================================
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