Le Saturday 30 July 2011 à 11:29:32PM, tdo.chem.ucsb.edu a écrit :
> Hi,
>
> I try to understand the format of the .dat force field parameter
> files. I have 2 questions:
>
> 1) In the DIHE (dihedral section), the parameters are reported in the form
>
> A-B-C-D x y z
>
> What are x, y and z?
>
> 2) Sometimes, when I build a frcmod file from parmchk (also use the
> flag -a Y to list out all parameters), the file contains different
> parameters of the same A-B-C-D, for example:
>
> c3-os-c3-os 1 0.850 180.000 -2.000
> c3-os-c3-os 1 1.350 180.000 1.000
>
> Is it true that these are for 2 different dihedral angles? If I change
> one of the OS in the PDB to OJ (a new atom type), how can I know which
> dihedral angle (out of the 2 above) contains my new OJ atom?
>
> Thank you,
>
> Thanh
Hi Thanh,
Look at the AMBER file formats page:
http://ambermd.org/formats.html#parm.dat
IPT , JPT , KPT , LPT , IDIVF , PK , PHASE , PN
[IJKL]PT atom types or wildcard for I and L
IDIVF factor by which the torsional barrier is divided
PK barrier height
PHASE phase shift angle (in degrees)
PN periodicity of the torsional barrier
(if PN .lt. 0.0 then the torsional potential is assumed to have more
than one term, and the values of the rest of the terms are read from the
next cards until a positive PN is encountered. The negative value of pn
is used only for identifying the existence of the next term and only the
absolute value of PN is kept)
torsional potential: (PK/IDIVF) * (1 + cos(PN*phi - PHASE))
--
Thomas Gaillard
Maître de conférences
Laboratoire de Biochimie
Ecole Polytechnique
91128 Palaiseau cedex
tel: +33 1 69 33 48 62
fax: +33 1 69 33 49 09
thomas.gaillard.polytechnique.edu
http://bioc.polytechnique.fr/~gaillard
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Received on Sun Jul 31 2011 - 05:00:03 PDT
