AMBER Archive (2002)

Subject: About counterions

From: Andrei Leitão (ierdna_at_yahoo.com)
Date: Thu Dec 05 2002 - 13:10:30 CST

 Dear AMBER user,

 I am doing some molecular dinamics from heptamers and I
had problems with the end base pairs (only one part was
very distorted - about 90 degrees). I think that
counterions were important to the distortion because some
of them were very far from the phosphate backbone.
 Only Na+ counterions were included according to the
program xleap and the procedure used in the study was
similar to the tutorial (dA-dT).
 I have more one question: How can I change the mdcrd files
to the pdb files? I did not find it on the manual.
 Thank you very much,

=====
Andrei Leitão
Doutorando em Química Medicinal
Graduante Student in Medicinal Chemistry
NEQUIM - Núcleo de Estudos em Química Medicinal - Brasil
UFMG - Universidade Federal de Minas Gerais
NEQUIM - Medicinal Chemistry Group - Brazil
UFMG - Federal University of Minas Gerais

_______________________________________________________________________
Busca Yahoo!
O melhor lugar para encontrar tudo o que você procura na Internet
http://br.busca.yahoo.com/