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
>
> On 2/6/07, Yong Duan <duan.ucdavis.edu> wrote:
> >
> > There are two classes of force field parameters in amber, the "standard"
> > force fields for nucleic acids and amino acids (proteins) and the
general
> > force field for (general) organic compounds. The difference between
these
> > two classes of force fields is that the "standard" force fields have
been
> > "carefully" tuned specifically for nucleic acids and peptides and the
> > general ff tries to cover a wide range of chemical compounds. I'd
suggest
> > you start from either of these two. In you case, you may want to start
> from
> > the "general force field". Check the "antechamber" manual for detail and
> if
> > you have further questions please let us know. If your tests show that
the
> > parameters need further improvement, you can always improve later.
> >
> > Developing ff requires fairly elaborate calculations and is generally
> suited
> > for people with considerable experience, patience and persistence (i.e.,
> > stubbornness :) ). If you are relatively new to modeling, it may take
some
> > time to get it done right. Instructions over email are not sufficient.
> >
> > yong
> >
> > -----Original Message-----
> > From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
> Of
> > deepti nayar
> > Sent: Monday, February 05, 2007 9:37 PM
> > To: amber.scripps.edu
> > Subject: Re: AMBER: force fields
> >
> >
> > hi
> >
> > i have to carry out simulation of peptides containing
> > alpha,beta-dehydroamino acid residues. (basically dehydrophenylalanine
> > residues )bt before that i have to make force field for phe and del
> > phe residues. i have all the parameters (bond angle,bond
> > length,hybridisation) which are required for building force field for
> > phe and del phe residues.
> >
> > kindly tell me if there is any prevously available force field for phe
> > residue. i dont have any ides as to how to make a force field on my
> > own. kindly help
> >
> >
> > thanx
> > deepti
> >
> > On 2/5/07, Yong Duan <duan.ucdavis.edu> wrote:
> > >
> > > This is a bit unusual. Can you elaborate?
> > >
> > > yong
> > > -----Original Message-----
> > > From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On
Behalf
> > Of
> > > deepti nayar
> > > Sent: Sunday, February 04, 2007 11:05 PM
> > > To: amber.scripps.edu
> > > Subject: AMBER: force fields
> > >
> > >
> > > hi
> > >
> > > i am new to amber9. can any one plz guide me how to make a force
> > > field? i dont want to use inbuilt force fields of amber and so want to
> > > build a new one for my molecule myself.
> > >
> > > thanx
> > > deepti
> > >
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >
>
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Received on Wed Feb 07 2007 - 06:07:46 PST
