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
>
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Received on Wed Feb 07 2007 - 06:07:29 PST
