>>
> > Sir/madam,
> > I am the user of amber6.I have been trying to run minimization of a
>complex
> > (peptide in methanol) through Sander but so far I have been unsuccessful
>I
> > have added the methanol box from the BOSS41 and then changed its output
>into
> > amber6 format. Then I ran it through xleap to generate the topology file
>and
> > co-ordinate file.But then I have been unsuccessful.I have tried running
>the
> > whole system as a single complex in vaccum giving the option igb=3,But
>the
> > co-ordinate file which is formed after the minimization is not fully
> > formed.I would like to have your advice on this topic.
> > Thanking you,
> > amit
> >
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>
>----------------------------------------------------------------------------
>James W. Caldwell (voice) 415-476-8603
>Department of Pharmaceutical Chemistry (fax) 415-502-1411
>Mail Stop 0446 (email) caldwell_at_heimdal.ucsf.edu
>513 Parnassus Avenue (video)
>farbauti.compchem.ucsf.edu
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Received on Thu Oct 19 2000 - 14:39:41 PDT
