AMBER Archive (2007)

Subject: AMBER: Amber: Number density profile, pucker..reg

From: Praveena Gopal (gp_mqm_at_yahoo.com)
Date: Tue Jun 12 2007 - 01:17:37 CDT

Dear Amber users,

      I have run a 2ns simulation for a cyclic peptide consisting of six residues in explicit water (TIP3 model).

   Kindly help me with the following,

1) How to calculate the number density profile of all the backbone atoms along a particular axis.

2) How to obtain the number of water molecules that enter the cyclic peptide during the course of time.

3) I have seen a keyword pucker to study the puckering of five atoms. Is it correct if I select any five atoms randomly in the cyclic peptide to understand the puckering nature of the peptide ring.

Thank you,

Regards,
G. Praveena

 
 
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