Hi Andrew,
What you have is correct for a dual topology approach, but it may not be
the best approach for the single topology path which is generated with
1b_leap.sh. The issue is the 1b_leap topologies loaded and put in m1 and m2
may have dummy atoms. I haven't run the sidechain tutorial so I'm not sure,
but if they do have dummy atoms then you'll end up with slightly different
end states. If you need a single topology approach then what Hannes has
outlined in the multistepping section should work?
Best,
Dan
On Wed, Dec 13, 2017 at 11:17 AM, Andrew Schaub <aschaub.uci.edu> wrote:
> Good Morning,
>
> I followed the A9 tutorial updated by Dr. Hannes Loeffler. In the sidechain
> tutorial there are not explicit steps for -q (decharge), +vdw, +q
> (recharge) steps. I've been trying to adapt the ligand tutorial to the
> sidechain tutorial, so I can do the three explicit steps with a sidechain.
> My goal is to do *single topology* of an alanine to valine like the
> tutorial, but to do the three explicit steps.
>
> For script 1b_leap.sh, can I just do the following change at the end:
>
> # decharge transformation
> decharge = combine {m1 m1 w}
> setbox decharge vdw
> savepdb decharge proteins_decharge.pdb
> saveamberparm decharge proteins_decharge.parm7 proteins_decharge.rst7
>
> decharge = combine {m1 m1 ligand w}
> setbox decharge vdw
> savepdb decharge complex_decharge.pdb
> saveamberparm decharge complex_decharge.parm7 complex_decharge.rst7
>
> # recharge transformation
> recharge = combine {m2 m2 w}
> setbox recharge vdw
> savepdb recharge proteins_recharge.pdb
> saveamberparm recharge proteins_recharge.parm7 proteins_recharge.rst7
>
> recharge = combine {m2 m2 ligand w}
> setbox recharge vdw
> savepdb recharge complex_recharge.pdb
> saveamberparm recharge complex_recharge.parm7 complex_recharge.rst7
>
> So I repeat m1 in the decharge, and repeat m2 in the recharge. My next step
> would be to do tiMerge
>
> loadRestrt protein.rst7
> setOverwrite True
> tiMerge :1-162 :163-324 :99 :261
> outparm merged_protein.parm7 merged_protein.rst7
> quit
> _EOF
>
> $parmed complex.parm7 <<_EOF
> loadRestrt complex.rst7
> setOverwrite True
> tiMerge :1-162 :163-324 :99 :261
> outparm merged_complex.parm7 merged_complex.rst7
> quit
>
> Is that how we would set it up, so we could have three explicit steps? Any
> information/guidance would be appreciated.
>
> Best Regards,
>
> Andrew
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>
--
Daniel J. Mermelstein, Ph.D candidate
McCammon & Walker Groups
Department of Chemistry & Biochemistry
University of California, San Diego
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Received on Sun Dec 17 2017 - 15:00:02 PST
