Yes, add to the leap.in file the following line:
charge UNK
On Mon, 11 Apr 2011, Baptiste Legrand wrote:
> Dear all,
>
> I classically use amber and antechamber to solve NMR structures of
> exotic molecules with repeated motifs. Nevertheless, for a molecule with
> numerous motifs, I can't use antechamber because the molecule have 200+
> atoms. So I generate a mol2 with Sirius (with the Gaff atom type) and
> use the frcmod of the small molecules with identical motifs to start a
> simulation. But the generated prmtop files in this case do not have
> charges (zero) as my initial mol2 file do not have charges too.
>
> Is there a command in leap to calculate the charges as antechamber?
> There is my typical script:
>
> #antechamber -i C4.mol2 -fi mol2 -o ./prep/C4.prepin -fo prepi -c bcc -s
> 2 > ./prep/antechamber.out
> cat > leap.in <<EOF
> source leaprc.gaff
> source leaprc.ff99SB
> UNK=loadmol2 C6.mol2
> loadamberparams C4.frcmod
> saveamberparm UNK ./prep/C6.prmtop ./prep/C6.inpcrd
> quit
> EOF
> tleap -f leap.in > ./prep/leap.out
>
> Thanks,
> Best wishes,
> Baptiste
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------
Dr. Hector A. Baldoni
Area de Quimica General e Inorganica
Universidad Nacional de San Luis
Chacabuco 917
5700 San Luis - Argentina
hbaldoni.unsl.edu.ar
---------------------------------------
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Received on Mon Apr 11 2011 - 08:00:03 PDT
