[gmx-users] pdb2gmx error

[Justin A. Lemkul]

Quoting Tawhid Ezaz <ezaztaw at yahoo.com>:

> I am sorry, my previous mail bounced back, as it was over 50 KB.
>
> I changed the ffG43a1 to include the GTP and GDP which I got from a previous
> post here. {http://www.gromacs.org/pipermail/gmx-users/2005-May/015188.html}
>
> I  changed some structure like giving comment with ; as the origicanal # was
> giving error. but now it tells me there is an error that 05* is not found in
> the atom type database.
>
>
>
> Program pdb2gmx, VERSION 3.3.1
> Source code file: resall.c, line: 148
>
> Fatal error:
> Atom type O5* (residue GTP) not found in atomtype database
> -------------------------------------------------------
>
>
>
> I am including the file here .the GTP residue is at the bottom of the file.
>
>
> 	     https://netfiles.uiuc.edu/tezaz2/shared/ffG43a1.rtp
>
> Is there any other GTP and GDP residue for the force field 43a1?

Have a look at the other entries in the .rtp file, and notice how the formatting
of the GTP molecule you entered looks nothing like the others.  Use the format
of other residues to guide you (paying special attention to similar molecules,
like ATP, which is already a part of ffG43a1).  The information in the file you
found appears to be in a different format, although you may still be able to
extract information from it.

Alternatively, you could use the PRODRG beta server to generate a
suitably-formatted topology (which you can include as an .itp file in your
system topology).  However, this topology will require editting, as some of the
parameters (most notably charges) will likely be unsatisfactory.

-Justin

>
> Thanks in advance.
>
> 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 9:14:37 PM
> Subject: Re: [gmx-users] pdb2gmx error
>
> 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/
>
> ========================================
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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/

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