Dear
All,
I
'm now trying to prepare a structure and get the prmtop and inpcrd
input files for MD simulation. I wrote all operation in below:
1
from a mol2 file, create a gaussin input using antechamber:
antechamber
-i n-octane.mol2 -fi mol2 -o octane_gin.gjf -fo gzmat
2
Run the gaussian
3
antechamber -i octane_gin.out -fi gout -o octane.gaff.mol2 -fo mol2
-nc 0 -c resp -rn OAS
4
parmchk -i octane.gaff.mol2 -f mol2 -o octane.frcmod
5
antechamber -i octane.gaff.mol2 -fi mol2 -o octane.gaff.pdb -fo pdb
6
use packmol with octane.gaff.pdb for getting 500 molecules
7
xleap -f leaprc.gaff
8
octane = loadmol2 octane.gaff.mol2
9
loadamberparams octane.frcmod
10
OAS = loadpdb packmol.pdb
11
check OAS ( I got some errors and warnings )
12
saveamberparams OAS h.prmtop h.inpcrd ( leap couldn't create input
files )
I
want to do MD simulations for 500 octane molecules. Could you help me
for using packmol file in Amber ?
Could
you please help me to get prmtop and inpcrd files succesfully with
leap ?
Thanks
in advance
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Received on Fri Dec 05 2008 - 16:43:35 PST
