Dear prof. Case,
thanks for your additional comment !
Of course I was thinking about 4 atoms which
satisfy the right bond criteria, but thanks
also for your suggestions regarding that more
general cases.
Best wishes,
Marek
Dne Wed, 27 Feb 2013 21:25:27 +0100 David A Case
<case.biomaps.rutgers.edu> napsal/-a:
> On Wed, Feb 27, 2013, Marek Maly wrote:
>>
>> So if one would like to add some improper torsion to group of 4 atoms
>> with known Amber atom types,
>
> I don't really agree with the previous answers. There isn't any way to
> add
> such a term as a part of the force field, since tleap will only make
> improper
> terms for a central atom bonded to exactly three other atoms. If you
> have an
> arbitrary group of 4 atoms (that doesn't fit the bonded criterion), you
> may be
> able to treat it as an "NMR" torsion restraint (although the functional
> form
> of a restraint term is not the same as the usual dihedral terms in the
> force
> field.)
>
> The other option is to edit the prmtop file (either manually, or perhaps
> via
> ParmEd) to add in the terms you want.
>
> ...good luck....dac
>
>
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Received on Wed Feb 27 2013 - 13:00:03 PST
