Re: problem at maintaining geometry coordinate

Date: Mon Aug 23 2010 - 05:11:45 CDT

Quoting Kwee Hong <>:

> ... I've done some adjustment to the parameter file (
> par_all22_prot.inp <>).
> ...
> ...The Cd-S bond length has
> become more than 0.6nm. According to experiment, the bond length and bond
> angle should be as follow:
> Cd-S(terminal) 0.2467nm
> Cd-S(bridging) 0.2560nm
> S-CD-S 109.5°
> Cd-S-C 95.5°


To start with, in your "modpar" file you set the force constant of
Cd-S(...) bond(s) to 0.00, so no wonder you got such big 'deviations'
[look for the physical meaning of each term of the force-field formula
in the literature]. Besides, I don't see any entry in the "modpar" for
bond angles or dihedrals around the CAD atom. So, did you really set a
formal bond between the cadmium and the sulfur(s) in your topology
file?!? [if you did, the program should complain about the absence of
the angle and dihedral terms...]


Elsa S. Henriques                     e-mail:
Investigadora Auxiliar
Biologia Estrutural e Computacional (@CNC)
e Grupo de Química Estrutural (@CCC)
Cv15 - RMB Lab
Departamento de Química - Universidade de Coimbra
3004-535 COIMBRA                         Portugal
Tel.: +351 23 9852080 - ext.417
Fax : +351 23 9827703

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