From: Alsaloum, Matthew (matthew.alsaloum_at_yale.edu)
Date: Sun Oct 18 2020 - 21:06:58 CDT
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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