VMD-L Mailing List

From: Babban Mia (babbanmia_at_gmail.com)
Date: Sat Aug 13 2011 - 21:39:41 CDT

No Worries

I just centered my protein and solvent first doing this :

#center protein

mol new protein.psf

mol addfile protein.pdb

set everyone [atomselect top all]

[atomselect top all] moveby [vecmul {-1 -1 -1} [measure center $everyone]]
[atomselect top all] writepdb protein_center.pdb

#center solvent

mol new solv.psf

mol addfile solv.pdb

set everyone [atomselect top all]

[atomselect top all] moveby [vecmul {-1 -1 -1} [measure center $everyone]]
[atomselect top all] writepdb solvent.pdb

and then simple used the vmd gui to solvent using non standard solvent
,works great!

I had thought the VMD SOLVATE GUI would handle the centering by itself but
seems that it does not

Thanks again everyone

Best
Babban

On Sun, Aug 14, 2011 at 7:45 AM, Babban Mia <babbanmia_at_gmail.com> wrote:

> 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.
>>>
>>
>>
>