VMD-L Mailing List

From: Babban Mia (babbanmia_at_gmail.com)
Date: Sat Aug 13 2011 - 07:10:18 CDT

Hello

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

Best
Babban

On Fri, Aug 12, 2011 at 4:21 PM, Babban Mia <babbanmia_at_gmail.com> 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