[AMBER] How to use parmed in Amber20 tools

From: <neildancer.sina.com>
Date: Wed, 18 Aug 2021 20:22:14 +0800

Dear, Amber experts
     When I try to go through the thermodynamic intergration tutorial of side-chain mini (http://ambermd.org/tutorials/advanced/tutorial9/#sidechain_mini), some weird problems had been appeared frequently. For example, the parmed.py script was not found in the amber20 folder. Maybe this script was replaced by Parmed package, or not, I'm not sure that. Then, I decided to try to use the Parmed package to merge the topologies and coordinates file without any parameter modificaion on the original input file that be from the turtorial, this error had been appeared:
ValueError: <Cmap; <Atom C [3150]; In LYS 222>--<Atom N [425]; In THR 25>--<Atom CA [427]; In THR 25>--<Atom C [437]; In THR 25>--<Atom N [-1]>; type=<CmapType; resolution=24>> is not in list .
I don't know how to fix it. Please help me.
My parmed inputs was following:
parmed protein.parm7 <<_EOFloadRestrt protein.rst7setOverwrite TruetiMerge :1-198 :199-396 :25 :223outparm merged_protein.parm7 merged_protein.rst7quit_EOF
parmed complex.parm7 <<_EOFloadRestrt complex.rst7setOverwrite TruetiMerge :1-198 :199-396 :25 :223outparm merged_complex.parm7 merged_complex.rst7quit_EOF



Ning Wang <PhD>
National Laboratory of Biomacromolecules
Institute of Biophysics, Chinese Academy of Sciences

My reseached interests has foucsed on protein structure determinated by Cryo-EM, virtual screening of potential drugs, protein molecular dynamic simulation, and protein design via computational biology.

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Received on Wed Aug 18 2021 - 05:30:03 PDT
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