Hi,
I want to get topology and co ordinate files of a modified residue.In order
to this I have made frcmod and .lib(using Xleap) file for the modified
residue of cysteine named as CYP,but after loading the force-field file and
CYP.lib file whenever I go to load the pdb file,leap gives the result that
none of the atoms are present in the residue template and thus at the time
of saving topology file fatal errors come as none of the atoms has any known
atom type.
please help me.
On Sat, Sep 3, 2011 at 8:59 AM, Jason Swails <jason.swails.gmail.com> wrote:
> On Fri, Sep 2, 2011 at 6:20 AM, madhumita das
> <madhumita.bioinfo.gmail.com>wrote:
>
> > Hi all the Amber users,
> >
> >
> > I have created a library file for a new
> > residue CYP(modified Cysteine: CysSHg+) I have done this according to
> amber
> > tutorial,but whenever I go to save topology and coordinate files in xleap
> > as
> > saveAmberParm CYP CYP.prmtop
> > CYP.prmcrd
> > following error comes.
> > Improper number of arguments!
> > Usage: <unit> <topologyfile>
> > <coordfile>
> >
>
> This error message is pretty clear. You need to supply a file name for the
> input file. Try this:
>
> saveamberparm CYP CYP.prmtop CYP.inpcrd
>
>
> >
> > Can anyone help me where I am doing wrong? What should be the correct
> > approach to get topology and coordinate files from library file?
> >
> >
> >
> > Yours faithfully,
> >
> > Madhumita Das
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Sep 05 2011 - 14:30:06 PDT
