[AMBER] T.I. Sidechain setup (softcore potential) based off of A9 tutorial

From: Andrew Schaub <aschaub.uci.edu>
Date: Wed, 13 Dec 2017 11:17:58 -0800

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

$parmed complex.parm7 <<_EOF
loadRestrt complex.rst7
setOverwrite True
tiMerge :1-162 :163-324 :99 :261
outparm merged_complex.parm7 merged_complex.rst7

Is that how we would set it up, so we could have three explicit steps? Any
information/guidance would be appreciated.

Best Regards,

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Received on Wed Dec 13 2017 - 11:30:03 PST
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