Re: H-H bond in solvate

From: Jorge Pikunic (jorge.pikunic_at_bioch.ox.ac.uk)
Date: Sat Jul 30 2005 - 09:35:13 CDT

I just checked and, as far as I can see, solvate 1.2 does not include
the "auto none" statement when building water segments. Shouldn't it
disable generation of bonds and dihedrals for building TIP3 water
segments?

Thank you,

Jorge

On Sat, 2005-07-30 at 14:57, Jorge Pikunic wrote:
> Hello,
>
> 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,
>
>
> Jorge
>
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:39:45 CST