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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Received on Tue Jun 21 2011 - 06:30:04 PDT
