I
completely did the operations below to prepare a structure and get
the prmtop and inpcrd input files for MD simulation :
1
from a mol2 file, create a gaussin input using antechamber:
antechamber
-i n-octane.mol2 -fi mol2 -o octane_gin.gjf -fo gcrt
2
Run the gaussian
3
antechamber -i octane_gin.out -fi gout
-o octane.gaff.mol2 -fo mol2 -nc 0 -c resp -rn HEP
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
created a residue 'HEP' but I didn't save it as a lib file so I
didn't load a lib file into leap. And also I couldn't send a mail
includes my packmol pdb file to amber.scripps.edu.
Isn't it possible to
attach a pdb file to the mail ? The packmol pdb file I created does
not have TER cards betwen each separate molecules.
Could
you please help me to get prmtop and inpcrd files succesfully with
leap ?
Thanks
in advance
--- On Tue, 12/2/08, David A. Case <case.biomaps.rutgers.edu> wrote:
From: David A. Case <case.biomaps.rutgers.edu>
Subject: Re: AMBER: using packmol file in Amber
To: amber.scripps.edu
Date: Tuesday, December 2, 2008, 6:14 AM
On Tue, Dec 02, 2008, oguz gurbulak wrote:
> FATAL: Atom .R< HEP 1>.A<C1 1> does not have a type.
Have you created a residue library called "HEP" and loaded into LEaP?
Generally, you need to post *exactly* what you did in order to get much useful
help.
...dac
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Received on Fri Dec 05 2008 - 18:28:28 PST
