All of these files can be downloaded from Section 3.2 of the online tutorial
(
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section2.htm).
All of the files necessary to run this MMPBSA.py calculation can be
downloaded on that site as part of the tarball near the top of the page
called Est_Rec_top_mdcrd.tgz.
I hope that helps.
-Bill
On Fri, Apr 8, 2011 at 1:01 PM, vani panguluri <vanipanguluri.gmail.com>wrote:
> Hello,
>
> In the MMPBSA.PY in protein- ligand complex how can I get the
> *1err.solvated.prmtop
> that *file i had done the prod steps as shown in the manual but i got
> stucked over this step
> $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
> 1err.solvated.prmtop -cp complex.prmtop -rp receptor.prmtop -lp
> ligand.prmtop -y *.mdcrd
>
> Can anyone explain me in detail about this step and how to get those files
>
> Regards,
> Vani
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Fri Apr 08 2011 - 10:30:12 PDT
