On Mon, Apr 11, 2011 at 7:29 AM, Baptiste Legrand <bap.legrand.gmail.com>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:
>
*calculate* the charges? No. leap doesn't calculate charges. Your best
bet is to break up your system into residues and build charges for each of
those residues independently. You can use R.E.D. tools for this.
Good luck,
Jason
>
> #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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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Apr 11 2011 - 10:00:02 PDT
