[AMBER] Question about INTRAmolecular restraint

From: Lorenzo Gontrani <l.gontrani.caspur.it>
Date: Fri, 10 Jun 2011 18:52:29 +0200

Dear all, I would like to run a simulation of an ionic liquid with
nitrate anions.
I have several X-Ray data that are well interpreted by my simulations.
The only problem is probably due to the fact that the anion is
partially pyramidalized during the simulazion (300K), and that N-O
distance of GAFF force field is too short w.r.t to X-Ray data. So, I
would like to apply an intramolecular distance restraint and/or an
improper dihedral restraint (out of plane). I performed some
restrained simulations in the past, but all of them regarded proteins
with NOE restraint between couple of protons. In my case I have to
apply the restraint to ALL nitrates in my simulation cell. Shall I
simply replicate the same restraint for every residue (i. e. to
prepare a complete DISANG file with some script)? Or do the new
keywords of Amber10 allow the use of a more complex masks? I read a
couple of e-mails that suggested not to use them.
Any hint will be very appreciated!

Regards to all


 Lorenzo Gontrani
 Research associate of EDXD group
 University of Rome "La Sapienza"
 GSM +39 338 7615798
 Email l DOT gontrani AT caspur DOT it
 Webpage: http://webcaminiti/gontrani.html
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Received on Fri Jun 10 2011 - 10:00:03 PDT
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