trying to generate a peptide

From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Tue Oct 25 2005 - 20:07:01 CDT

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Hi all,
Now I'm trying to generate a hexapeptide using a
previoulsy created pdb file and psfgen.

Here's the sequence of the peptide:

Ace-Arg-Tyr-Tyr-Arg-Trp-Arg-NMe

psfgen tells me there is no such residue as NMe or
Ace. I'm using top_all22_prot.inp, and there is an a
PRES ACE present. However, there is NO topology for
NMe, which is NH-CH3.

The molecule should have 150 atoms. Can anybody
provide any assistance in generating the "correct"
residues ACE and NMe? (ACE is CH3-C=O)

Thanks in advance,
Richard

p.s. I've succeeded in minimizing my protein and now
I'm running 1020000 steps (1020 ps) of dynamics.

                
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