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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Received on Mon Apr 11 2011 - 07:30:03 PDT
