About Amber force fields

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Sat Jan 19 2008 - 08:54:30 CST

As I am carrying out MD of protein complexes embedded in POPC and other
membranes built with VMD, I would like to make use of NAMD. My question is:

While Paratool pluging is being adapted to general use thanks to Jan Saam,
which is the present status of NAMD with respect to carrying out MD with Amber
force fields (which I am currently using)? Specifically, I make use of ff99SB
for the protein, while the non-polymeric organic ligands are based on GAFF ff
(Antechamber). I.e., I am stuck at a single residue for the ligand, which is
not the best in case of large ligands as in my studies. Does the
inter-compatibility ff99SB/GAFF hold for NAMD as well? At any event, I would
consider that latter as a transition before Paratool.

I really posed a more restricted question on the same subject long ago. Now I
have acquired experience with MD on such systems, which means that I may be
better prepared to the shift.

Thanks

francesco pietra

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