**From:** *ehenriques_at_qui.uc.pt*

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

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Quoting Kwee Hong <joyssstan0202_at_gmail.com>:

*> ... I've done some adjustment to the parameter file (
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*> par_all22_prot.inp <http://birg1.fbb.utm.my/joyce/modpar.html>).
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*> ...
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*> ...The Cd-S bond length has
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*> become more than 0.6nm. According to experiment, the bond length and bond
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*> angle should be as follow:
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*>
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*>
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*> Cd-S(terminal) 0.2467nm
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*> Cd-S(bridging) 0.2560nm
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*>
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*> S-CD-S 109.5°
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*> Cd-S-C 95.5°
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*>
*

Hi,

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...]

E.

-- Elsa S. Henriques e-mail: ehenriques_at_qui.uc.pt 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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