Re: [AMBER] Question about INTRAmolecular restraint

From: Jason Swails <>
Date: Fri, 10 Jun 2011 22:43:42 -0600

It sounds like some of those can be added directly to the force field via an
frcmod file (i.e. improper dihedrals). The others, just use the NMR
restraints and replicate it for each residue you want to apply it to if the
frcmod won't do the trick (or doesn't apply to your case).

You can also override GAFF force field definitions via an frcmod file if it
turns out they're not what they should be for your system.


On Fri, Jun 10, 2011 at 10:52 AM, Lorenzo Gontrani <>wrote:

> 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
> --
> =======================================
> 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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Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Fri Jun 10 2011 - 22:00:03 PDT
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