[gmx-users] popc

[Justin A. Lemkul]

Quoting Chiara Parravicini <parravicini.chiara at gmail.com>:

> 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?

I wouldn't expect the gd_* to match between ffG53a6 and ffG43a2x, since ffG43a2x
was likely developed before ffG53a6 (hence the numbering).  If you have a look
at ffG43a1-c.tdb, you'll notice that the bonded parameters are comparable.

I would imagine that if the .hdb file was formatted in such a way that it can no
longer be used, I would suspect the .tdb files would suffer the same
consequences.  My first reaction is that the .tdb and .hdb files will be the
only ones that have to be re-formatted, however, I could be wrong.

You could probably start over with any of the other Gromos force fields if you'd
like, although I don't think the re-formatting would take too much time.

> What about the "atomtype 'CA' not found!" error?

There are several discussions about such things in the list archive.  If you
search for your error in conjunction with terms like "lipid," "membrane," etc.
you should turn up some results about how to deal with it.

-Justin

>
> 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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>



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

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/

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