[gmx-users] Atom Types, grompp problem!!
feenstra at few.vu.nl
Wed May 11 13:18:59 CEST 2005
David van der Spoel wrote:
> On Wed, 2005-05-11 at 11:47 +0100, Una Bjarnadottir wrote:
>>David thanks for your respone!!
>>I changed the files like you said but than grompp complained about next
>>new atom type in the ATP complex, CS1. I added in 9 of the 47 atom
>>types to the .atp file in share/gromacs/top dir and I'm wandering if
>>they have all been replaced like OS to OA and where I could find
>>information about the new names if grompp will complain about the rest?
IMHO, there thould be no need to add atom types to the 43a1 forcefield
for ATP. There are already basepairs in the forcefields, so there are
atom types as well that should at least be reasonably appropriate. If
you do choose to add atom types, be aware that this is a highly
non-trivial modification/addition to the forcefield, which will require
extensive well-validated (re-)parameterization.
In addition, there are recent new versions of the Gromos forcefields
(vis., the 45a3 and 53a5/6 versions), in which also (some of the) DNA
parameters have been improved. See recent papers by Oostenbrink & Van
Gunsteren. These parameter sets are already available from the Gromacs
website, Topologies, Forcefields. Use with care, there is no guarantee
that all parameters match those published exactly (although, should and
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