From: Ajian (ajian.he_at_hit.edu.cn)
Date: Tue Jan 11 2022 - 22:59:51 CST
Dear Moumita,
Thank you very much! I can not localize the dihe.txt file in the CHARMM_GUI outcome package, I think it is the issue of the CHARMM_GUI, maybe I need make a dihedral restraint file by myself.
Best,
Thank you.
Ajian
Sent from Mail for Windows
From: Moumita Saharay
Sent: Wednesday, January 12, 2022 12:01 PM
To: namd-l_at_ks.uiuc.edu; Ajian
Subject: Re: namd-l: FATAL ERROR: sed: can't read restraints/dihe.txt: No suchfile or directory
Dear Ajain,
It is clear from the error message that NAMD is unable to locate restraints/dihe.txt file.
Please give a proper path for the same.
best,
Moumita
On Wed, Jan 12, 2022 at 5:45 AM Ajian <ajian.he_at_hit.edu.cn> wrote:
Dear all,
I followed the CHARMM-GUI video demo of free energy calculator: relative ligand binder for membrane systems (https://urldefense.com/v3/__https://charmm-gui.org/?doc=demo&id=fec&lesson=7__;!!DZ3fjg!oDhla4YCA0fTNwhWrr8V5Eysk_ILVgrbVex21bqXXCPz0H7XPZlGB6dR46BleEovyw$ ), and got all the files needed to run NAMD. I tar the zip file in my working folder and enter into the ligand or complex folder and follow the instruction,
./1_mkdir.pl
./2_mkconf.pl
Looks normal, however when I run bash file
#!/bin/bash
cnt=1
while [ ${cnt} -le 6 ]
do
namd2 equ_site_${cnt}.inp | tee equ_site_${cnt}.out
cnt=$[$cnt+1]
done
there is a fatal error mesg like this,
FATAL ERROR: sed: can't read restraints/dihe.txt: No such file or directory
while executing
"exec sed -e "s/\$FC/500/g" restraints/dihe.txt > restraints/$outputname.dihe"
(file "equ_site_1.inp" line 171)
I run it in my working station, not the cluster, my NAMD version is NAMD_2.14_Linux-x86_64-netlrts
Any help or suggestion?
Thank you.
Ajian
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-- Dr. Moumita Saharay Assistant Professor, Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, India
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