VMD-L Mailing List

From: Babban Mia (babbanmia_at_gmail.com)
Date: Sat Aug 13 2011 - 21:15:32 CDT

Thanks Dr. Axel

I did not notice the color change while loading input pdb/psf file. The
input was indeed broken because as you had suggested earlier that segment
ids should not be same for doing the solvation,I tried changing the segment
ids through a python script and it had failed at some places ,hence the
pdb/psf files were broken at some places.

I have resolved that thing for now and I tried solvating a small peptide
with non standard solvent pdb/psf box. but using the vmd gui ,I cant seem to
get the protein to the center of the box.

Is there a way to do it tk console /or in solvate gui plug in only ?

Thanks again

Best
Babban

On Sat, Aug 13, 2011 at 7:17 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

>
>
>
>
> 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>
> akohlmey_at_gmail.com> wrote:
>
>> On Sat, Aug 13, 2011 at 8:10 AM, Babban Mia < <babbanmia_at_gmail.com>
>> 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>
>> 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>akohlmey_at_gmail.com <http://goo.gl/1wk0>
>> http://goo.gl/1wk0
>>
>> Institute for Computational Molecular Science
>> Temple University, Philadelphia PA, USA.
>>
>
>