VMD-L Mailing List

From: Alexandre Suman de Araujo (asaraujo_at_if.sc.usp.br)
Date: Thu Oct 08 2009 - 16:19:26 CDT

Hi All

I'm using psfgen to generate the topology to beta-cyclodextrin using
charmm carbohydrate parameters obtained from this site:
http://mackerell.umaryland.edu/CHARMM_ff_params.html.

When I load the generated psf in VMD the total charge of the model is
about 60! The problem is that the names used in the parameters file are
bigger than the associated field and the number at the end of atom type
is read as the atom charge (the next field). For example, the CC3161
atom type have 0.09 as charge in the parameter file but VMD read its
charge as 1.0 (because de number 1 at the end), the CC3162 have a charge
of 2.0 (because de number 2 at the end) associated to it instead of 0.34
as defined in the parameter file.

Did anyone also deal with this problem??? I think the solution is to
change all names in the parameters files, but if someone have a smarter
solution I appreciate to know it.

Cheers 

-- 
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Alexandre Suman de Araujo                                    *
Faculdade de Ciências Farmacêuticas de Ribeirão Preto        *
Universidade de São Paulo                                    *
Dep. de Física e Química                                     *
Grupo de Física Biológica     * e-mail: asaraujo_at_fcfrp.usp.br*
Av. do Café, s/n°             * e-mail: ale.suman_at_gmail.com  *
CEP: 14040-903                * Phone: +55 (16) 3602-4172    *
Ribeirão Preto, SP, Brasil    * Phone: +55 (16) 3602-4222    *
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