AMBER Archive (2008)

Subject: AMBER: using packmol file in Amber

From: oguz gurbulak (gurbulakoguz_at_yahoo.com)
Date: Tue Nov 25 2008 - 09:49:19 CST

        
        
        
        
        
        

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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