VMD-L Mailing List

From: Jorge Pikunic (jorge.pikunic_at_bioch.ox.ac.uk)
Date: Wed Jul 27 2005 - 14:25:09 CDT

Hi,

I just noticed 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?

Thank you,

Jorge