RE: trying to generate a peptide

From: Michel Espinoza-Fonseca (
Date: Wed Oct 26 2005 - 03:35:23 CDT

The actual patch you need to apply is ACE and CT3 (the first one for acetylated N-terminus, the last one for N-Methylamide C terminus).
Here is an example on how to automatically patch the termini of your peptide:
topology toppar/top_all27_prot_na.inp
segment HPEP { pdb your_file.pdb
first ACE
last CT3
coordpdb your_file.pdb HPEP
writepdb your_output_file.pdb
writepsf your_output_file.psf
And that's all.
Hope it helps,


From: on behalf of Richard Wood
Sent: Tue 10/25/2005 8:07 PM
Subject: namd-l: trying to generate a peptide

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:


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,

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

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