how to perform MD with two proteins

From: Mert Gür (
Date: Sun Dec 02 2007 - 08:37:18 CST

I have generated two simple peptides in hyperchem and merged them here to an
single pdb.
peptide 1: asn asp met phe arg leu
peptide 2: leu leu phe met gln his
As I am generating the psf file in VMD as given in the tutorial the second
peptide is destroyed.
Can anybody help me with that problem.
Or if you have advices how to model this two peptides in NAMD that would
help also.
Thanks in advance
Mert Gür
Koc University/Istanbul

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