[gmx-users] pdb2gmx -inter automatised ?
fufezan at uni-muenster.de
Tue Aug 12 15:26:59 CEST 2008
"pdb2gmx .... < inter.txt" did the trick. Although it was a bit
painful to generate the inter.txt in the first instance :)
Dr. Christian Fufezan
Westfälische Wilhelms-Universität Münster
Institut für Biochemie und Biotechnologie der Pflanzen (IBBP)
48143 Münster - Germany
Tel: ++49 251 8324791
Fax: ++49 251 8328371
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:
> 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.
>> 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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before
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