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
> >
>
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Received on Wed Feb 07 2007 - 06:07:34 PST
