Sajad Ahrari wrote:
thanks felix
you are right.both exist.but how can i tell gromacs to put MG ions in
the standard vicinity of ATP? or maybe gromacs knows it already and i
have to just type "MG-ATP" instead of "ADP"?
If all residues, including ligands and cofactors, exist in the .rtp database,
all you need to do is run the structure through pdb2gmx and it will produce a
topology. Note that the presence of .rtp entries is a key caveat; pdb2gmx isn't
magic and won't work for anything you provide as input. But in the case that
everything is in place for a given force field, then there should be no problem.
Try it and report back with specific errors if they arise. Spending too much
time on the hypothetical gets nothing accomplished :)
-Justin
------------------------------------------------------------------------
*From:* "Rausch, Felix" <frau...@ipb-halle.de>
*To:* Discussion list for GROMACS users <gmx-users@gromacs.org>
*Sent:* Wed, April 27, 2011 1:33:52 PM
*Subject:* [gmx-users] MG-ATP
Hi.
Looking at the list of building blocks available in GROMACS
(http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blocks?highlight=building+blocks)
you can find ATP as well as MG. So having a ATP-MG-complex in your
simulation shouldn't be a problem.
Regards,
Felix
------------------------------------------------------------------------
*Von:* gmx-users-boun...@gromacs.org im Auftrag von Sajad Ahrari
*Gesendet:* Mi 27.04.2011 10:52
*An:* gromacs user forum
*Betreff:* [gmx-users] MG-ATP
dear users
is "MG-ATP" known to gromacs ? in my pdb structure I have ADP and MG,
apart from each other and not being crystallized in the right place. can
i omit them and replace ADP's with MG-ATP? or I should introduce this
topology to gromacs?
regards
sajad
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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