[gmx-users] popc

[Chiara Parravicini]

Thank you for your advice!
I reformatted the ffG43a2x.hdb file, but now pdb2gmx is complaining about
the ffG43a2x-n.tdb file, that is different from the ffG53a6 one, and
probably it would complain also for ffG43a2x-c.tdb. Here, also the fields
gd_* don't match.  Is there the way to use the existing topologies with
another gromos force field instead of reformatting all the ffG43a2x* files?
What about the "atomtype 'CA' not found!" error?

On Fri, Mar 21, 2008 at 12:57 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> Quoting Chiara Parravicini <parravicini.chiara at gmail.com>:
>
> > Dear gromacs users,
> >
> >  I would like to perform  simulations of a protein embedded in popc,
> using a
> > force field of the gromos series and I downloaded popc.pdb, popc.itp,
> > lipid.itpa and the force field ffG43a2x extended for lipids.
> > Looking throughout the archive I found different suggestions, but none
> of
> > them help me to successfully perform my simulations:
> >
> > - Using the ffG43a2x* force field, when I run pdb2gmx on the popc.pdb, I
> get
> > this error:
> >
> >  Fatal error:
> >
> > Error in hdb file ffG43a2x.hdb:
> >
> > Wrong number of control atoms (2 iso 3) on line:
> >
> > 1 1 N -C CA
>
> Right; I think the format of the .hdb file changed somewhere along the
> way, and
> ffG43a2x is formatted in the old style.  What pdb2gmx is complaining about
> is
> that it thinks it is trying to add an atom named 'N', with reference atoms
> of
> -C and CA.  Compare the ffG43a2x.hdb with, say, ffG53a6.hdb, and you will
> see
> the difference.  The first atom specified must be the name of the hydrogen
> atom
> you wish to add, so that line should be something like:
>
> 1   1   H   N   -C   CA
>
> For more on .hdb files, read the manual, section 5.5.2.
>
> -Justin
>
> >
> >   - If I manually write a topology file for the ffG43a2x force field and
> > submit it to grompp to write a .tpr, I get this error:
> >
> >  Fatal error:
> > Atomtype 'CA' not found!
> >
> >   In the topology file I included both lipid.itp and popc.itp, and I
> > commented the following lines in the lipid.itp file as suggested:
> >
> >  [ defaults ]
> >
> > 1 1
> >
> >  - I also tried to add the different sections [ atomtypes ], [ pairtypes
> ],
> > etc... of the lipid.itp files to ffG53a5* files, but I still get the
> error:
> >
> >  Atomtype 'CA' not found!
> >
> >  Does anybody know what I miss? Is there a way to resolve this problem
> and
> > use popc with ffG53a5 or ffG43a2x?
> >
> >  All comments are very appreciated!
> > Thanks in advance!
> >
> >  Chiara
> >
>
>
>
> ========================================
>
> 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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