Dear Dac,
I am posting the mol2 file of raloxifene (PDB-1ERR). I am also giving you
the exact sequence of commands that i used and the files generated after
each command.
1) Input *ral.mol2*
command: $AMBERHOME/bin/parmchk -i ral.mol2 -f mol2 -o ral.frcmod
output ral.frcmod
2) Input ral.frcmod
command: $AMBERHOME/bin/tleap -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
>source leaprc.gaff
> RAL= loadmol2 ral.mol2
> check RAL
> loadamberparams ral.frcmod
> saveoff RAL ral.lib
> saveamberparm SUS ral.prmtop ral.inpcrd
> exit
I obtained* ral.lib, ral.prmtop, ral.inpcrd. *Next i created the complex of
raloxifene with protein solvated and neutralized it in the following way.
command: $AMBERHOME/bin/tleap -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
>source leaprc.gaff
> loadamberparams ral.frcmod
*
*
*
*
On Mon, Sep 17, 2012 at 11:40 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Mon, Sep 17, 2012, Shomesankar Bhunia wrote:
>
> > I have carried a GAMESS geometry optimization using GAMESS. I have used
> > the gamess output (log file) to fit RESP charges using RED-vIII.5 tools
> > and finally i generated a *.mol2 file that i used in the generation of
> > .prmtop and .inpcrd files by the same way as shown in tutorial B4 at
> amber
> > tutorials (http://ambermd.org/tutorials/basic/tutorial4b/).
> > I used GAFF and used Leap in the generation of the .prmtop and .inpcrd
> > files.Thanks in advance.
>
> Can you post the mol2 file? We also need the exact sequence of LEaP
> commands
> you used, and the frcmod file (if any) that was specific to your molecule.
> Basically, we need to be able to reproduce the problem in order to try to
> fix
> it.
>
> ...thx...dac
>
>
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Received on Tue Sep 18 2012 - 01:00:04 PDT
