VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Aug 13 2011 - 08:22:08 CDT

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.