Thanks David, I know the usual way. It's just that I am testing my
application "ACPYPE" with sleap and unfortunately still failing.
Cheers,
Alan
On 21 June 2011 14:26, David A Case <case.biomaps.rutgers.edu> wrote:
> On Fri, Jun 17, 2011, Alan wrote:
> >
> > sleap -f sleap.in
> >
> > Warning: cannot find template for residue DMP in our library.
> > I am going to construct the template by myself.
> > OK. I have fixed bond order and added hydrogens.
> > Now I am calling antechamber to assign atom type and partial
> > charge.
> >
> >
> >
> > Total number of electrons: 302; net charge: 0
> >
> > Running: /Users/alan/Programmes/amber11/bin/sqm -O -i sqm.in -o sqm.out
> >
>
> If the "fastbld" option of sleap doesn't work, then run antechamber by
> hand:
>
> antechamber -i dmp.pdb -fi pdb -o dmp.mol2 -fo mol2 -c bcc
>
> followed by
>
> parmchk -f mol2 -i dmp.mol2 -o dmp.frcmod
>
> Then you can load the dmp.mol2 and dmp.frcmod files into LEaP, and go from
> there.
>
> ...good luck....dac
>
>
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--
Alan Wilter S. da Silva, D.Sc.
Bioinformatician, UniProt - PANDA, EBI-EMBL
CB10 1SD, Hinxton, Cambridge, UK
+44 1223 49 4588
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Received on Wed Jun 22 2011 - 02:00:04 PDT
