From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Aug 13 2011 - 08:47:57 CDT

On Aug 13, 2011, at 9:42 AM, Babban Mia <babbanmia_at_gmail.com> wrote:

I do not understand that how and where the input is broken.The psf and pdb
looks completely normal to me

Well they are not.

I already told you that you can easily see it from visualizing them. How
much more proof do you need??

Axel

Perhaps you could tell me that
Thanks

Babban

On Sat, Aug 13, 2011 at 6:52 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Sat, Aug 13, 2011 at 8:10 AM, Babban Mia <babbanmia_at_gmail.com> wrote:
> > 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.
>
> it is not the plugin that doesn't work,
> it is you input that is broken!
> it is very easy to see from visualizing it,
> and you get a _ton_ of error messages.
>
> if you feed VMD incorrectly formatted files,
> it won't do want you want it to do. if you
> ignore error messages and expect to get
> the right result, then you are in the wrong business.
>
> garbage in -> garbage out.
>
>
> axel.
>
> > 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
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>