Please read AMBER manual (
http://amber.scripps.edu/doc9/index.html). The
manual also comes with the package. This is analogous to starting from ABC
when you learn to read. First, go through the sections on tleap/leap/xleap.
You will also be able to find the information on the topology file format.
If you do not understand what the manual says, post the specific questions
or read the relevant papers and the textbooks. Thank you!
yong
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
deepti nayar
Sent: Tuesday, February 06, 2007 2:34 AM
To: amber.scripps.edu
Subject: Re: AMBER: force fields
hi
i got to know about topology file. i found it on net
thanx for the help
deepti
On 2/6/07, deepti nayar <deepti.icgeb.gmail.com> wrote:
> thanx so much yong. i will begin my work wid it. one more thing i
> would like to ask . how to build a topology file? if i use already
> available force fields, i will have to make changes in topology to
> suit it to my peptide. can u plz tell me as to how to make topology
> file. i have gone through various topology files preent in amber9 but
> im not able to understand the format. like what does DUMM stands
> for?and varous odr thngs like OMIT , INT.
>
>
> i would be pleased if u can help me .
>
> thanx
> deepti
>
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Received on Wed Feb 07 2007 - 06:07:40 PST
