Andy Somogyi wrote:
Any suggestions for programmatically repairing the pdb, i.e. Guessing the missing residue atoms and adding them at the appropriate coordinates?
I tried vmd's autopsf, which works, but evidently vmd's implementation of charm27 is different than Gromac's, it adds atom types n
Any suggestions for programmatically repairing the pdb, i.e. Guessing the
missing residue atoms and adding them at the appropriate coordinates?
I tried vmd's autopsf, which works, but evidently vmd's implementation of
charm27 is different than Gromac's, it adds atom types not present in Gromac'
On 2012-03-23 05:39:38PM -0400, Justin A. Lemkul wrote:
>
>
> Andy Somogyi wrote:
> > Hi All,
> >
> > I'm trying to generate topology for a PDB from viperdb, PDB ID 1DZL,
> > http://viperdb.scripps.edu/info_page.php?VDB=1dzl
> >
> > using
> >
> > pdb2gmx -f 1dzl_full.pdb -o test.pdb -p test.
Andy Somogyi wrote:
Hi All,
I'm trying to generate topology for a PDB from viperdb, PDB ID 1DZL,
http://viperdb.scripps.edu/info_page.php?VDB=1dzl
using
pdb2gmx -f 1dzl_full.pdb -o test.pdb -p test.top
I've tried CHARMM27 and AMBER03 FFs, water none and I get the result:
Fatal error:
At
Hi All,
I'm trying to generate topology for a PDB from viperdb, PDB ID 1DZL,
http://viperdb.scripps.edu/info_page.php?VDB=1dzl
using
pdb2gmx -f 1dzl_full.pdb -o test.pdb -p test.top
I've tried CHARMM27 and AMBER03 FFs, water none and I get the result:
Fatal error:
Atom CG is used in the topo
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