>
> 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
> > quit
>
> 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
> > loadoff ral.lib
> > complex = loadpdb 1ERR_A_H.pdb
> > solvate complex TIP3PBOX 10.0
> >charge complex # it was found to be -10.0000 so i added 10 Na+ in
> the next step
> > addions Na+ 10
> >saveamberparm complex 1ERR_1.prmtop 1ERR_1.inpcrd
> >savepdb complex 1ERR_1.pdb
> >quit
>
> I obtained solavted 1ERR_1.prmtop, 1ERR_1.inpcrd, and 1ERR_1.pdb. I copied
> the files to NAMD folder. I am also attaching the NAMD config script.
>
Thanks in advance.
>
>
>
>
>
>
>
> 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
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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- application/octet-stream attachment: ral.mol2
Received on Tue Sep 18 2012 - 01:00:05 PDT
