[gmx-users] pdb2gmx -inter automatised ?

[Tsjerk Wassenaar]

Hi :)

Maybe these little scripts are useful...

The first, titratable.sh (use: titratable.sh file.pdb), generates a
list of residues for which the protonation state can be set, including
the termini. The second, gmxquery.sh (use: titratable.sh file.pdb |
gmxquery.sh) gives a series of 0 1 2, according to the protonation
states desired. So,

titratable.sh file.pdb | gmxquery.sh | pdb2gmx -f file.pdb -inter

should be close to what you want. The output from titratable.sh can
also be modified prior to piping it through gmxquery. And that can be
easily scripted :)

Do note that it doesn't deal with SS bonds.

Hope it helps,

Tsjerk

On Tue, Aug 12, 2008 at 3:26 PM, Christian Fufezan
<fufezan at uni-muenster.de> wrote:
> Ok,
>
> "pdb2gmx ....  < inter.txt" did the trick. Although it was a bit painful to
> generate the inter.txt in the first instance :)
>
> Thanks again
>
> Christian Fufezan
>
>
> Dr. Christian Fufezan
> Westfälische Wilhelms-Universität Münster
> Institut für Biochemie und Biotechnologie der Pflanzen (IBBP)
> Hindenburgplatz 55
> 48143 Münster - Germany
>
> Tel: ++49 251 8324791
> Fax: ++49 251 8328371
> Web: http://www.fufezan.net
>
> On Aug 11, 2008, at 20:33 , Justin A. Lemkul wrote:
>
>>
>>
>> Christian Fufezan wrote:
>>>
>>> Dear gmx users,
>>> I am new to MD and working my way through some tutorials. I saw that
>>> pdb2gmx has the "-inter" flag which is used to specify which
>>> conformers/protonation stats should be used.
>>> Is there a way in which this can be automatised ?
>>> For example, lets say I have a list.txt
>>> ....
>>> HIS A 105 -> HISB
>>> ....
>>> and I would like to use that list for all runs to be used.
>>
>> Would this be useful:
>>
>> http://wiki.gromacs.org/index.php/Making_Commands_Non-Interactive
>>
>> Trying to automate this procedure using -inter is probably a lot more work
>> than actually interacting with pdb2gmx.  If you're happy with the default
>> protonation states of all the other titratable sites (check pdb2gmx -h),
>> then you can use -his instead, which might de-complicate things.  Otherwise,
>> you have to know the order of all the interactively selected residues, which
>> protonation state to give them, and how many of each you have.
>>
>> -Justin
>>
>>> Thanks in Advance
>>> Christian Fufezan
>>> _______________________________________________
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>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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