AMBER Archive (2008)

Subject: Re: AMBER: using packmol file in Amber

From: oguz gurbulak (gurbulakoguz_at_yahoo.com)
Date: Tue Dec 02 2008 - 08:02:59 CST

        
        
        
        
        
        

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_at_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_at_biomaps.rutgers.edu> wrote:
From: David A. Case <case_at_biomaps.rutgers.edu>
Subject: Re: AMBER: using packmol file in Amber
To: amber_at_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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