VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Aug 14 2011 - 00:09:28 CDT

On Sat, Aug 13, 2011 at 10:39 PM, Babban Mia <babbanmia_at_gmail.com> wrote:
> No Worries

of course not. this has been _your_ problem, not mine.

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

rule number one when using a computer:
the computer does what you _tell_ it to do.
nothing more, nothing less. it does _not_
do what you _think_ it _should_ do.
if you rely on a computer being smarter
than you and trust that it does the right
thing when you are not certain what is the
right thing to do, then you are in big trouble.

that does not only apply to using VMD,
but to _anything_ that is done with a computer.
i strongly suggest you respect that in the future.

cheers,
     axel.

>
> 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>
>>> 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.
>>>
>>
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.