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
> > >
> >
> > -----------------------------------------------------------------------
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> >
>
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Received on Wed Feb 07 2007 - 06:07:33 PST
