From: Babban Mia (
Date: Sat Aug 13 2011 - 07:10:18 CDT


Has anybody been able to check this problem?
I am still trying it with vmd solvate plug in GUI and it does not work.
Would appreciate any feedback on it.

Thanks again


On Fri, Aug 12, 2011 at 4:21 PM, Babban Mia <> wrote:

> Hello Everyone
> I was well on my way to obtain a good solvated box for my protein using
> SOLVATE PLUG IN GUI in VMD but then I am facing an unknown problem with the
> solvate plug in in VMD[GUI].
> Whenever I am trying to solvate my protein with a non standard solvent,It
> seems to be considering only the first 10 water/or any other solvent
> molecules and then rest of all the solvent molecules vanishes.
> I attach the
> 1. Protein (protein.pdb & protein.psf)
> 2. Solvent (solvent.pdb & solvent.psf)
> and the topology file(topology.inp)
> I have done a lot of googling and I have still not come to know what is
> causing this problem.I will be grateful if somebody could try and do the
> solvation with the attached files and check for the errors.
> The size of the solvent.pdb BOX is 40A
> Best regards
> Babban