Hi Tawhid,
The file you got was in the format used by the _program_ GROMOS. But this
format is not supported by pdb2gmx/Gromacs. The GROMOS _forcefield_ is a set
of equations and parameters, which stands apart from the formatting of the
building blocks. You could've at least taken a bit of effort to look at the
other building block definitions, and you would've seen the differences.
Also, the fact that you got complaints about "#" should have been indicative
to you that you were doing something wrong. In regards the building blocks
(the .rtp file), read Chapter 5 (notably 5.5). This should help you to
convert the GROMOS format building block to a Gromacs format one.
Tsjerk
On Nov 28, 2007 1:34 AM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
> Quoting Tawhid Ezaz <[EMAIL PROTECTED]>:
>
> > 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 <[EMAIL PROTECTED]>
> > To: Discussion list for GROMACS users <gmx-users@gromacs.org>
> > Sent: Monday, November 26, 2007 9:14:37 PM
> > Subject: Re: [gmx-users] pdb2gmx error
> >
> > Quoting Tawhid Ezaz <[EMAIL PROTECTED]>:
> >
> > > 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 <[EMAIL PROTECTED]>
> > > To: Discussion list for GROMACS users <gmx-users@gromacs.org>
> > > Sent: Monday, November 26, 2007 7:14:43 PM
> > > Subject: Re: [gmx-users] pdb2gmx error
> > >
> > >
> > > 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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> > >
> > >
> > >
> > >
> >
> >
> >
> > ========================================
> >
> > 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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> >
> >
> >
> >
>
>
>
> ========================================
>
> 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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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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