VMD-L Mailing List

From: Alexandre Suman de Araujo (asaraujo_at_if.sc.usp.br)
Date: Thu Jul 30 2009 - 14:48:13 CDT

Hi all

I'm trying to build the psf (using autopsf) of a b-cyclodextrin (a cyclic
polymer) using the top_all36_carb.rtf topology file which contains the
alpha-D-glucose monomer topology.

The problem is that in the monomer topology there are two hydrogen atoms bind to
oxygens which linkage each monomer on cyclodextrin. Moreover, the generated psf
superimpose two oxygens from each monomer in the linkage.

Does anybody can help me with this issue? Is it possible to handle this kind of
thing without editing the topology file or I will need to remove some atoms
from it? If yes, how should I handle the charge imbalance from this deletion?

Best regards 

-- 
Alexandre Suman de Araujo
Instituto de Física de São Carlos
Universidade de São Paulo
São Carlos - Brasil
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