From: Axel Kohlmeyer (
Date: Thu Jul 31 2008 - 09:02:29 CDT

On Thu, 31 Jul 2008, Alan wrote:

AW> Hello List,

hello alan,


AW> vmd water.parm7 water.rst7
AW> and VMD displays my waters as "triangles", i.e., with a extra bond
AW> between H-H. If loading pdb, all fine.
AW> Is there a way of avoiding this issue?

yes and no. the bond is there, because it is in the parm7 file.
amber needs this for the constraining the geometry of the water
molecules and of course VMD is true to what is in the file.

however, there is little that cannot be taken care of with some
tcl/vmd scripting. you can put the attached script code into your
.vmdrc or make it otherwise loadable by the tcl interpreter in
vmd and then just type the command "fixamberwater".

works just as well on CHARMM topologies with the same feature.


AW> Many thanks in advance.
AW> Alan
AW> --
AW> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
AW> Department of Biochemistry, University of Cambridge.
AW> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
AW> >><<

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.