topology and parameter file for C17 H16 N2 O2 Br2

shen Lingling llshen at mail.shcnc.ac.cn
Wed Apr 25 08:20:51 EST 2001


Thanks very much for your reply.
Would you please tell me what the value means 
in the dihedral definition in parameter file
( value 750.00)? 
As to my case, I'd defined all dihedral angels for 
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 
change something else such as the value 750.00?
Again, what is the final evaluation of the FF I got from 
xplo2d? Does you mean that the minimition procedure 
offered in *_min.inp is enough?
BTW, my last e-mail was not meant to say somwthing 
about the program xplo2d. I am just a beginner and eager
to get a acceptable FF for my molecular. -:)

Yours

Lingling

=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 xplo2d.
>> 
>> 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 
>> in pdb file 1hni.pdb, then I found that the two benzene planes=
 are torsioned to
>> certain degree during optimization.
>> Of cause, the same happened to the top and par file get from=
 Hic-Up sever.
>> 
>> Doea such evaluation means that the wrong generating of force=
 field parameters 
>> for my molecular? and can I trust in such a force field to do=
 more simulations?
>
>****************************************************************=
**
>                        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.
>****************************************************************=
**

                    =D6=C2
=C0=F1=A3=A1

            shen Lingling
            llshen at mail.shcnc.ac.cn

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