Date: Tue Jul 27 2010 - 04:40:21 CDT
Quoting ipsita basu <ibasu788_at_gmail.com>:
> Hi all,
> I am running namd using NPT having system peptide embedded in
> lipid bilayer. I have the peptide with N and C terminal capped with
> formyl and ethanolamine . But during the simulation run the two capped
> groups are breaking from the peptide. Before simulation run I had
> restraints on peptide backbone.
Exactly how did you cap your terminal residues, i.e., which patches
(PRES) are you using? If, by ethanolamine you mean RESI ETAM in the
topology file, then this is a complete molecule per se, and by default
is not linked to other residues ... it would explain why it 'breaks'
during your simulation.
-- Elsa S. Henriques e-mail: ehenriques_at_qui.uc.pt Investigadora Auxiliar Biologia Estrutural e Computacional (@CNC) e Grupo de Química Estrutural (@CCC) Cv15 - RMB Lab Departamento de Química - Universidade de Coimbra 3004-535 COIMBRA Portugal Tel.: +351 23 9852080 - ext.417 Fax : +351 23 9827703
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