AMBER Archive (2006)

Subject: AMBER: residue and atom number

From: Andrea Bortolato (andrea.bortolato.1_at_unipd.it)
Date: Mon Jul 10 2006 - 07:57:05 CDT

Dear all,

I have to correctly set the noshakemask option
for my TI calculation.

The problem is that the residue number and the
atom number is different between the pdb file
created by ambpdb and the desc command in leap.

Looking in the mailing list (but it is a quite
old post
http://amber.ch.ic.ac.uk/archive/200205/0013.html)
I saw that for the residue I have to choose the
residue number presents in the pdb file and not
the one presents in the output of the desc
command.

Is the same for the atom number? Shall I use the
atom number in the pdb file generated by
the ambpdb command?

Thank you,
Andrea Bortolato

---------------------------------------
Andrea Bortolato, Ph.D. Student

Molecular Modeling Section
Department of Pharmaceutical Sciences
University of Padova,
Via Marzolo, 5
35131 Padova - ITALY
Phone: +39-049-8275801
Fax: +39-049-8275366 or +39-049-8275704
e-mail:andrea.bortolato.1_at_unipd.it
Webpage URL http://mms.dsfarm.unipd.it
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