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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