[AMBER] CHARMM Output - Empty Restraint File

From: Aanshi Gandhi <aanshi.gandhi.mail.utoronto.ca>
Date: Mon, 29 Mar 2021 15:46:46 +0000


I’m trying to run an MD simulation using AMBER outputs from CHARMM-GUI and I seem to be having some problems with my restraint files (.rest). I’ve attached the files for your consideration. A breakdown of what is happening:

The minimization step worked fine. The first equilibration step; there’s a command in the README file to do: if (-e dihe.restraint && ${cnt} < ${cntmax}) sed -e "s/FC/${fc[${cnt}]}/g" dihe.restraint > ${istep}.rest. However, I got an error when I ran this on Beluga but when I removed the if command and just submitted it as: sed -e "s/FC/{'250.0', '100.0' , '50.0' , '50.0' , '25.0'}/g \ sed 's/"[[:space:]]\+"/","/g" dihe.restraint > step6.1_equilibration.rest, it ran properly but it gave me an empty .rest file but a new file with the right information. Then, in the second equilibration step, I ran the same command as above and it ran completely fine except the .rest file was empty and there was no other file with the right information. However, the third equilibration step still ran without problems except again no .rest file.

I would really appreciate any insight you may have on what I can do to fix this issue. I have attached my submit script for the second equilibration step (submit3.sh), the equilibration input file (step6.2_equilibriation.mdin), the empty rest file (step6.2_equilibration.rest), the output file (step6.2_equilibriation.mdout) and the README file from CHARMM.

Thank you,
Aanshi Gandhi (she/her)
M.ASc Candidate, Garton Lab
Email<mailto:aanshi.gandhi@mail.utoronto.ca> | LinkedIn<https://www.linkedin.com/in/aanshigandhi/>

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Received on Mon Mar 29 2021 - 09:00:02 PDT
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