H-H bond in solvate

From: Jorge Pikunic (jorge.pikunic_at_bioch.ox.ac.uk)
Date: Sat Jul 30 2005 - 08:57:59 CDT


It seems that water molecules generated using the solvate plugin do not
have the H-H bond that CHARMM uses (TIP3 water). Is it because it does
not use "auto none"?

I am generating water segments like this (following NAMD manual):
segment W {
 auto none
 residue 1 TIP3

and using solvate like this:
package require solvate
solvate crystal.psf crystal.pdb -t 12 -o solvated

Is there anything wrong? If not, why does solvate not add the H-H bond?

Thank you,


This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:41:00 CST