[gmx-users] pdb2gmx error

[Justin A. Lemkul]

Quoting Tawhid Ezaz <ezaztaw at yahoo.com>:

> 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.
>
> http://www.gromacs.org/pipermail/gmx-users/2005-May/015188.html
>
> 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?

That depends entirely upon what your errors are and what you're trying to do. 
Please provide more details.

-Justin

>
> Thanks a lot for your help.
>
> Tawhid
>
>
>
> ----- 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
>  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
> jalemkul at vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
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>
>



========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

========================================