Re: structure breaking

Date: Tue Jul 27 2010 - 04:40:21 CDT

Quoting ipsita basu <>:

> 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:
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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