From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Mon Oct 19 2020 - 14:01:33 CDT
Hi Matt,
What kind of machine are you running on? sed and tr are standard UNIX
command line tools that NAMD/CHARMM-GUI is trying to use to make its own
life easier. It would be weird if a Mac of a Linux system didn't have these
tools, but I'm betting you are running on a Windows system that doesn't
have these tools, and NAMD is erroring because you don't have those tools
available.
-Josh
On Sun, Oct 18, 2020 at 8:15 PM Alsaloum, Matthew <matthew.alsaloum_at_yale.edu>
wrote:
> Hi all,
>
> I hope you are all doing well! I am new to molecular dynamics and NAMD and
> am having some trouble getting a configuration file to work. NAMD has
> worked on very simple configuration files I have written in the past while
> learning the ropes, but I currently have a protein-lipid-water-ion system
> made via CHARMM-GUI with a pre-written configuration file that keeps giving
> me fatal errors that I believe all stem from problems reading Tcl code. I
> have searched through the Wiki, User Guide, and previous mailing threads
> and cannot find an answer to this question (apologies if I missed it), so I
> would appreciate any input!
>
> The beginning of my file reads as:
>
> structure step5_charmm2namd.psf
> coordinates step5_charmm2namd.pdb
>
> set temp 310.15;
> set outputname step6.1_equilibration;
>
> # read system values written by CHARMM (need to convert uppercases to
> lowercases)
> exec tr "\[:upper:\]" "\[:lower:\]" < ../step5_assembly.str | sed -e "s/
> =//g" > step5_charmm2namd.str
> source step5_charmm2namd.str
>
>
> ^^ However, when I run NAMD, I get an error:
>
>
> TCL: couldn't execute "tr": no such file or directory
> FATAL ERROR: couldn't execute "tr": no such file or directory
> while executing
> "exec tr "\[:upper:\]" "\[:lower:\]" < ../step5_assembly.str | sed -e "s/
> =//g" > step5_charmm2namd.str"
> (file "step6.1_equilibration.inp" line 8)
> FATAL ERROR: couldn't execute "tr": no such file or directory
> while executing
> "exec tr "\[:upper:\]" "\[:lower:\]" < ../step5_assembly.str | sed -e "s/
> =//g" > step5_charmm2namd.str"
> (file "step6.1_equilibration.inp" line 8)
>
> If I manually comment out this line (which probably isn't the correct
> thing to do...), I get similar errors later on in the script. For example,
> this portion of the file:
>
> # planar restraint
> exec sed -e "s/Constant \$fc/Constant 5/g" step5_charmm2namd.colvar.str >
> restraints/$outputname.col
> colvars on
> colvarsConfig restraints/$outputname.col
>
> Returns an error:
>
> TCL: couldn't execute "sed": no such file or directory
> FATAL ERROR: couldn't execute "sed": no such file or directory
> while executing
> "exec sed -e "s/Constant \$fc/Constant 5/g" step5_charmm2namd.colvar.str >
> restraints/$outputname.col"
> (file "step6.1_equilibration_commented.inp" line 157)
> FATAL ERROR: couldn't execute "sed": no such file or directory
> while executing
> "exec sed -e "s/Constant \$fc/Constant 5/g" step5_charmm2namd.colvar.str >
> restraints/$outputname.col"
> (file "step6.1_equilibration_commented.inp" line 157)
>
> Does anyone know why this error is occurring? I think there's something
> wrong with the syntax of the command, because "tr" and "sed" should be
> commands, not directories or files, to my knowledge. Thanks in advance for
> your help!
>
> Sincerely,
> Matt
>
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