[gmx-developers] pdb2gmx termini treatment

Berk Hess hess at cbr.su.se
Mon Feb 1 12:56:33 CET 2010


I just committed a relatively small, but important change to the way
pdb2gmx treats termini.
Now atoms ran be renamed, using the [ replace ] entry. This works also
if they are
not present in the normal residue rtp entry and also pdb files without
the atom present
will still be processed without problems.
This allows the second terminal oxygen, OXT, to be retained and renamed,
instead of always deleting and rebuilding it, as was done up till now.

The main reason for implementing this feature is that now the Amber
force field
can be added without the need of termini databases.

This update required some reordering of the pdb2gmx operation on the
input atom names
and the rtp entries. I have tested it a bit, but there are too many
possibilities for nasty input pdb files.
If people have some nasty files lying around and have time to test the
new git master code
and modified Gromos and OPLS database files, please go ahead and report



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