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
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Received on Thu Dec 05 2002 - 11:10:30 PST
