topology problem!

From: ramya wwjd (
Date: Fri Mar 09 2007 - 03:04:58 CST

hello sir,

I am working on hydrogenase(1FEH.pdb) and have to perform MD-Simulations by
NAMD. But the main problem I am facing with FES Clusters is that , these are
not present in the charmm topology file that i am using
(top_all27_prot_lipid.inp). when i generate psf and pdb by using psfgen, the
clusters were removed from the output pdb. Should I use some different
topology file for these clusters? and if so, how can i make this? can you
suggest? I will be greatful to you.
Thank you,

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