RE: trying to generate a peptide

From: Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Wed Oct 26 2005 - 03:35:23 CDT

Hi,
 
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
guesscoord
writepdb your_output_file.pdb
writepsf your_output_file.psf
 
And that's all.
 
Hope it helps,
 
Michel

________________________________

From: owner-namd-l_at_ks.uiuc.edu on behalf of Richard Wood
Sent: Tue 10/25/2005 8:07 PM
To: namd-l_at_ks.uiuc.edu
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:

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.

               
__________________________________
Yahoo! FareChase: Search multiple travel sites in one click.
http://farechase.yahoo.com

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:41:17 CST