AMBER Archive (2009)

Subject: [AMBER] Parmchk wrongly calculates missing parameters (fwd)

From: Gijs Schaftenaar (schaft_at_cmbi.ru.nl)
Date: Fri Feb 20 2009 - 07:16:17 CST

In parmchk.c missing parameters are estimated (see formula 5, gaff
publication),
however the D in the formula (dparm in parmchk.c) is wrongly calculated in
parmchk.c:

         dparm = (bondlength1 - bondlength2) * (bondlength1 - bondlength2);
         dparm =
                 dparm / (bondlength1 + bondlength2) * (bondlength1 +
bondlength2);

This is equivalent to :

(bl1 - bl2) * (bl1 - bl2) / (bl1 + bl2) * (bl1 + bl2) =

{ (bl1 - bl2) * (bl1 - bl2) / (bl1 + bl2) } * (bl1 + bl2) =

(bl1 - bl2) * (bl1 - bl2)

This is clearly wrong. The force constants calculated this way however do have
the correct magnitude. Which makes me inclined to think that the empirical
form of the expression was optimized with the wrongly calculated D's.
The error made in the calculation in D was corrected in part by the constant
used in the formula: 143.9.

Has this been noted before and if so what should be the correct constant in the
formula when it is correctly calculated.

Dr Gijs Schaftenaar
Computational Drug Discovery Group
CMBI, Radboud University Nijmegen
The Netherlands

     +----------------------------------------------------------------+
       Gijs Schaftenaar, Dr. | Computational Drug Discovery, CMBI
       Email: | Radboud University of Nijmegen
       G.Schaftenaar_at_ncmls.ru.nl | Medical Centre / NCMLS, route 260
       Tel. : +31 24 3619674 | Geert-Grooteplein 28
       Fax : +31 24 3619395 | 6525 GA Nijmegen, The Netherlands
     +----------------------------------------------------------------+

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