scopio a écrit :
>
> Dear AmberUsers:
>
> I have a pdb contains some residue that could not be recognized by xleap
> due to lacking of amber parameters. Fortunately, I get these parameters
> from a very kind person. But I don't know how to use them. Could anybody
> check them attached and give me some suggestions? Thanks in advance!
>
> By the way, is the mail reflector would filter email larger than 1MB?
>
> Regards!
>
> scopio
>
> ------------------------------------------------------------------------
> #
> #
> # quinone7.prm
> # cromofo_last.prm
> #
> #
> BOND
> #fe+mg ( k from CHARMM; dist from X-ray)
> nb fe 65.00 2.10
> o2 fe 65.00 2.25
> nb mgc 65.00 2.25
> ........................( igored )
> END
> BENDINGS
> #fe+mg
> cr nb mgc 0.00 0.00
> nb mgc nmh 0.00 0.00
> nb mgc ns 0.00 0.00
> ....................... ( igored )
> END
> TORSION PROPER
> #fe
> x fe nb x 0.00 4
> x fe o2 x 0.00 4
> ....................... ( igored )
> END
> TORSION IMPROPER
> x ccs ns mgc 1.100 2.0 180.0 cosine
> x x nmh mgc 1.100 2.0 180.0 cosine
> ...................... ( igored )
> END
> NONBONDED MIXRULE
> #fe
> fe 0.740 0.250 0.740 0.250 55.847
> #my
> mgc 0.650 0.250 0.000 0.000 24.305
> nh 1.824 0.170 0.000 0.000 14.010
> ns 1.824 0.170 0.000 0.000 14.010
> ...................... ( igored )
> END
>
> ------------------------------------------------------------------------
> RESIDUE bcl ( Total Charge = 0.0 )
> atoms
> group
> mg mgc 0.1340
> group
> cha csb 0.0650
> group
> chb cab -0.2240
> hb ha0 0.1150
> group
> chc cab -0.2730
> hc ha0 0.1680
> ............. ( igored )
> end
>
> bonds
> nb mg nc mg nd mg na mg
> nb c1b c1b c2b c2b c3b c3b c4b
> c4b nb
> nc c1c c1c c2c c2c c3c c3c c4c
> c4c nc
> nd c1d c1d c2d c2d c3d c3d c4d
> c4d nd
> na c1a c1a c2a c2a c3a c3a c4a
> c4a na
> ................ ( igored )
> imphd
> #
> c1b c4b nb mg
> c2b nb c1b chb
> c1b c3b c2b cmb
> c4b c2b c3b cab
> c3b nb c4b chc
> ................ ( igored )
> end
>
> termatom * *
> RESIDUE_END
you've got to save the parameters in a filename.pcy then in xleap do
:loadamberparams filename.pcy
--
M. J.Fernandez Carmona
Laboratoire ASI. Equipe Chimiométrie et Modélisation
Faculté des Sciences. Université de Nice Sophia-Antipolis
F 06108 Nice Cedex 2. France
tel : 33/(0)4 92 07 61 26 fax : 33/(0)4 92 07 61 25
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Received on Wed Mar 17 2004 - 07:53:00 PST
