Thanks a lot, Jason! I don't know why I didn't think of modifying the
force field..it is actually the easiest way!
Regards
Lorenzo
2011/6/11 Jason Swails <jason.swails.gmail.com>:
> 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.
>
> HTH,
> Jason
>
> On Fri, Jun 10, 2011 at 10:52 AM, Lorenzo Gontrani <l.gontrani.caspur.it>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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
=======================================
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 Sat Jun 11 2011 - 13:00:03 PDT
