[cnsbb] Re: topology and parameter file for C17 H16 N2 O2 Br2

Gerard "DVD" Kleywegt gerard at xray.bmc.uu.se
Thu May 3 13:23:46 EST 2001


 DIHEdral OX13 PX9  OX12 PX5     750.0 0   180.00

the '750' is the force constant (in this case, a very
high one, so the restraint is very strong)

--gerard


On 25 Apr 2001 llshen at mail.shcnc.ac.cn wrote:

> Thanks very much for your reply.
> Would you please tell me what the value means=20
> in the dihedral definition in parameter file
> ( value 750.00)?=20
> As to my case, I'd defined all dihedral angels for=20
> planar atoms and it still goes more planar torsion
> than those phenyl groups in animo acid whose parameters
> were defined by CHARMM force field. Do I need to=20
> change something else such as the value 750.00?
> Again, what is the final evaluation of the FF I got from=20
> xplo2d? Does you mean that the minimition procedure=20
> offered in *_min.inp is enough?
> BTW, my last e-mail was not meant to say somwthing=20
> about the program xplo2d. I am just a beginner and eager
> to get a acceptable FF for my molecular. -:)
>=20
> Yours
>=20
> Lingling
>=20
> =D4=DA 01-4-24 17:09:00 =C4=FA=D0=B4=B5=C0=A3=BA
> >xplo2d (http://xray.bmc.uu.se/usf/xplo2d_man.html#H6)
> >really works on the basis of the garbage-in,garbage-out
> >principle. you provide a pdb file of your compound, and
> >the program uses the bonds lengths etc it finds to
> >define restraints. if the input geometry is poor, your
> >parameter file will also be poor. for instance, if a
> >bond that must be flat because of the chemistry has
> >a torsion angle of, say, 160 instead of 180 degrees,
> >xplo2d will not recognise it as 'flat' and will not
> >generate a restraint. if you download the program and
> >run it yourself, you have more flexibility than when
> >you use the HIC-Up server (where almost all settings
> >of the program are fixed). nevertheless, it is always
> >a good idea to use the minimisation input file that
> >xplo2d generates to do a quick geometry optimisation
> >with cns/xplor. the result will be the structure that
> >cns/xplor will attempt to obtain later on when you
> >include the compound in your x-ray or nmr model and
> >refine against experimental data. and you can of course
> >always edit the top and par files yourself, e.g. to
> >add extra dihedral or improper restraints, or to
> >alter the target values
> >
> >--gerard
> >
> >> I am really puzzled at how to evalate top and par file generated by xp=
lo2d.
> >>=20
> >> I generated top and par file from a quantum optimized structure of my =
molecular.
> >> Then I used the top and par files to optimize the crystal structure of=
 my molecular=20
> >> in pdb file 1hni.pdb, then I found that the two benzene planes are tor=
sioned to
> >> certain degree during optimization.
> >> Of cause, the same happened to the top and par file get from Hic-Up se=
ver.
> >>=20
> >> Doea such evaluation means that the wrong generating of force field pa=
rameters=20
> >> for my molecular? and can I trust in such a force field to do more sim=
ulations?
> >
> >******************************************************************
> >                        Gerard J.  Kleywegt
> >Dept. of Cell & Molecular Biology  Bolshevik University of Uppsala
> >                Biomedical Centre  Box 596
> >                SE-751 24 Uppsala  SWEDEN
> >
> >    http://xray.bmc.uu.se/gerard/  mailto:gerard at xray.bmc.uu.se
> >******************************************************************
> >   The opinions in this message are fictional.  Any similarity
> >   to actual opinions, living or dead, is purely coincidental.
> >******************************************************************
>=20
>                     =D6=C2
> =C0=F1=A3=A1
>=20
>             shen Lingling
>             llshen at mail.shcnc.ac.cn
>=20
> ---
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--gerard

******************************************************************
                        Gerard J.  Kleywegt
Dept. of Cell & Molecular Biology  Bolshevik University of Uppsala
                Biomedical Centre  Box 596
                SE-751 24 Uppsala  SWEDEN

    http://xray.bmc.uu.se/gerard/  mailto:gerard at xray.bmc.uu.se
******************************************************************
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
******************************************************************


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