VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Tue Dec 09 2014 - 19:44:20 CST

To be honest with you - from my understanding - even if someone did do it -
they wouldn't know the difference. Studying binding is tricky in itself -
so even if someone did this and got negative results and then went back and
kept the hydrogens -- i doubt that it would have caused much of a
difference - but sure - wait.

Good luck.

Best,
/A

On Wed, Dec 10, 2014 at 12:23 PM, Kshatresh Dutta Dubey <kshatresh_at_gmail.com
> wrote:

> Thank you very much Ashar for suggestion.
> During the MD we had already applied SHAKE, and the protein structure
> mainly depends upon heavy atoms/backbone, so deleting the hydrogen in pdb
> and then re-adding them using psfgen, and then minimizing hydrogen only, I
> think, should not affect the protein structure, however I am eagerly
> waiting for the suggestions. I am very curious to know that if someone did
> it then what is wrong?
> Although, MMTSB tool (convpdb.perl), can convert the pdb formats but it is
> more about my curiosity about above protocol.
> Waiting for more suggestions.
>
> Regards
> Kshatresh
>
> On Wed, Dec 10, 2014 at 12:50 AM, Ashar Malik <asharjm_at_gmail.com> wrote:
>
>> In your MD - you were already using SHAKE for your hydrogen atoms. So the
>> current representation of your system has emerged from that. I guess the
>> question you should be asking is that in the MD ( which is basically MM)
>> the area of your interest that you now want to resolve, i.e. where your
>> ligand is interacting how many hydrogens are at the interface, if there
>> aren't many, you could delete hydrogens, and add them all over again using
>> psfgen effectively creating a new PSF of your system. However, what would
>> be better is that you write a simple code that iterates over your PDB file
>> and changes atom types.
>>
>> e.g. look here:
>>
>>
>> http://www.chem.cmu.edu/courses/09-560/docs/msi/ffbsim/B_AtomTypes.html#639162
>>
>> or there is an another program that lists table for equivalance here:
>>
>> http://inka.mssm.edu/~mezei/intocham/intocham.html
>>
>> a little before the half way point on the above webpage.
>>
>> This would help you keep your atom's positions.
>>
>> Also - there should be programs, i think, which already achieve this.
>>
>> If you are interetsed in deleting and guessing positions again using
>> psfgen, that should be "OK" but you might want to wait till you hear back
>> from an expert in the list ---
>>
>> Good luck,
>>
>> Best
>> /A
>>
>> On Wed, Dec 10, 2014 at 4:39 AM, Kshatresh Dutta Dubey <
>> kshatresh_at_gmail.com> wrote:
>>
>>> Dear Users,
>>>
>>> I have amber generated trajectories and I am willing to take some
>>> snapshots for QM/MM calculation using chemshell that runs fine with charmm
>>> psf and pdb file. But the different nomenclature of hydrogen for charmm and
>>> amber is creating the problem from direct use of amber generated pdbs. Is
>>> it correct if I save the coordinates without H and then re-adding them in
>>> psfgen and going further for QM/MM calculations? Please suggest me about
>>> the appropriateness of this method.
>>>
>>>
>>> Regards
>>> Kshatresh
>>>
>>>