From: Moumita Saharay (moumitasaharay_at_uohyd.ac.in)
Date: Tue Jan 11 2022 - 21:59:56 CST
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!sE_IEnHiMOUa4fQXxG2NkD9QiXQPlXFW50N7jtf9hH602Tgsv3rMA_xW2e7MDcN__Q$
> <https://urldefense.com/v3/__https://charmm-gui.org/?doc=demo&id=fec&lesson=7__;!!DZ3fjg!tXUzyvR3-uG-ho3Fc7yGYLpEaV9Z_mVs0DGKzTDgao3pa8Q-seUuU0zzDw6kPsPNbA$>),
> 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
>
>
>
>
>
> Sent from Mail
> <https://urldefense.com/v3/__https://go.microsoft.com/fwlink/?LinkId=550986__;!!DZ3fjg!tXUzyvR3-uG-ho3Fc7yGYLpEaV9Z_mVs0DGKzTDgao3pa8Q-seUuU0zzDw7pmBUOqg$>
> for Windows
>
>
>
>
>
>
>
-- 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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