Rausch, Felix wrote:
Dear Gromacs users,
I would like so simulate a protein with phosphorylated amino acids with
Gromacs 4.5.3. To do so, I got the "ffG43a1p" forcefield available from
the user contributions section (subsection force fields) and adapted the
parameters given there to Gromos53a6.
The problem now is that they introduced a new atom type called "OP",
which I have to add to the atomtypes.atp of my modified force field. I
already read about problems of a modified atomtypes.atp here in the
mailing list, but I assumed the problems were sorted out with version 4.5.3.
Not entirely, but probably the post you saw related to an LP atomtype, which
appears to be a special case.
But if I add OP to the atom list, pdb2gmx works fine, but grompp is
raising the error
Program grompp, VERSION 4.5.3.
Source code file: toppush.c, line: 629
Fatal error:
Unknown atomtype CMET
which is quite strange because "CMET" isn't appearing in any file I'm
using. When I remove OP from the atom list, pdb2gmx is of course raising
an error, so I'm a bit stuck here...
grompp reads all the force field files and is finding something it doesn't like.
In 4.5.3, the proper capitalization should be "CMet," not "CMET," as it was in
old versions. Capitalization and other nomenclature has been standardized as of
version 4.5.3, so old files with outdated names cause errors.
-Justin
To cut a long story short: Is there any way to introduce a new atom type
to atomtypes.atp or do I have to parameterize the phosphorylated
residues with already presend atom types?
Thank you in advance,
Felix Rausch
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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