[chimera-dev] Following on new atom types.

[Jean-Didier Maréchal]

Hi,

I am following on Elisabeth's question on the 23rd of january regarding
setting up new atoms. I have added platinum (for cisplatinum) as a new atom
type and proceed as you recommended (calculate the charge on isolated
species and generate the covalent bond for the first coordination sphere of
the metal). I have though two questions:

1. when running the minimization I have the following message:

Atom whose IDATM type has no equivalent Sybyl type:
#-2147483648.-2147483648:1 at PT1-CPT (type: Pt)

Although the minimization still proceed, I'd like to do things right. Could
you tell me where I could change the sybyl atomtype. I looked with the idle
the idatmType of this atom and it gives me Pt+. I don't understand what is
wrong.

2. I'd like to rapidly change the charges of the cisplatinum using charges
calculated with ab initio calculations. I was thinking to change these
values from the idle changing the charge attribute previous to
minimization. Does it sound correct? What would be the easiest way you
would reckon?

Best regards,
JD


****************************
Dr. Jean-Didier Maréchal
Associate professor
The Computational Biotechnological Chemistry Team
Unitat de Química Física
Departament de Química
Universitat Autònoma de Barcelona
Edifici C.n.
08193 Cerdanyola (Barcelona)
Tel: +34.935814936
e-mail: JeanDidier.Marechal at uab.es
www: http://g <http://asklipio.qf.uab.es>ent.uab.cat/jdidier<http://ent.uab.es/jdidier>
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