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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