From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Jan 12 2022 - 08:32:55 CST
Or maybe, if you think this is a CHARMM-GUI issue, contact their forum?
On Wed, Jan 12, 2022 at 12:01 AM Ajian <ajian.he_at_hit.edu.cn> wrote:
> 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
> <https://urldefense.com/v3/__https://go.microsoft.com/fwlink/?LinkId=550986__;!!DZ3fjg!oDhla4YCA0fTNwhWrr8V5Eysk_ILVgrbVex21bqXXCPz0H7XPZlGB6dR46CyQ4e1KA$>
> for Windows
>
>
>
> *From: *Moumita Saharay <moumitasaharay_at_uohyd.ac.in>
> *Sent: *Wednesday, January 12, 2022 12:01 PM
> *To: *namd-l_at_ks.uiuc.edu; Ajian <ajian.he_at_hit.edu.cn>
> *Subject: *Re: namd-l: FATAL ERROR: sed: can't read restraints/dihe.txt:
> No suchfile or directory
>
>
>
> Dear Ajain,
>
>
>
> It is clear from the error message that NAMD is unable to
> locate restraints/dihe.txt file.
>
> Please give a proper path for the same.
>
>
>
> best,
>
> Moumita
>
>
>
> On Wed, Jan 12, 2022 at 5:45 AM Ajian <ajian.he_at_hit.edu.cn> wrote:
>
>
>
> Dear all,
>
>
>
> I followed the CHARMM-GUI video demo of free energy calculator: relative
> ligand binder for membrane systems (
> https://urldefense.com/v3/__https://charmm-gui.org/?doc=demo&id=fec&lesson=7__;!!DZ3fjg!p-WZK8cpHgHB71LlCVOrJCVPe9zdbF79GE1DWxJsFySkN6eLRSwr6qS8Acctt48l0g$
> <https://urldefense.com/v3/__https:/charmm-gui.org/?doc=demo&id=fec&lesson=7__;!!DZ3fjg!tXUzyvR3-uG-ho3Fc7yGYLpEaV9Z_mVs0DGKzTDgao3pa8Q-seUuU0zzDw6kPsPNbA$>),
> and got all the files needed to run NAMD. I tar the zip file in my working
> folder and enter into the ligand or complex folder and follow the
> instruction,
>
>
>
> ./1_mkdir.pl
> <https://urldefense.com/v3/__http:/1_mkdir.pl__;!!DZ3fjg!sE_IEnHiMOUa4fQXxG2NkD9QiXQPlXFW50N7jtf9hH602Tgsv3rMA_xW2e5N7DWsKg$>
>
> ./2_mkconf.pl
> <https://urldefense.com/v3/__http:/2_mkconf.pl__;!!DZ3fjg!sE_IEnHiMOUa4fQXxG2NkD9QiXQPlXFW50N7jtf9hH602Tgsv3rMA_xW2e74co1GbA$>
>
>
>
> 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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