swati patel wrote:
helo justin,
yess since i am dealing with a complex,so i generated protein topology
using gromos96 43a1 force fields and for ligands,obtained topology using
PRODRG which uses gromos 87 force fields.
How to obtain similar force fields topologies since PRODRG only works
with gromos87 force fields and in gromacs i choosed optipn (9)i.e.gromos
96 force fields.??
This is not true. There is a newer PRODRG server that creates topologies for
Gromos96. Their quality is not particularly high, as noted on this list on a
weekly basis, and in the literature. Please see the paper linked from:
http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips
-Justin
--
========================================
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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