[gmx-users] gibbs' free energy tutorial: help with write_mdp.pl

[Raag Saluja]

Hi!

Thank you so much for your previous reply to my mail regarding Gibbs' free
energy!

However, I'm stuck again..
I tried the tutorial. On giving the command:

perl write_mdp.pl em_steep.mdp


I get these errors:

Raags-MacBook-Pro:native tubulin gibbs Preetiwadhwa$ perl write_mdp.pl
em_steep.mdp

Backslash found where operator expected at write_mdp.pl line 1, near "rtf1\"

Backslash found where operator expected at write_mdp.pl line 1, near "ansi\"

Backslash found where operator expected at write_mdp.pl line 1, near
"ansicpg1252\"

Backslash found where operator expected at write_mdp.pl line 1, near
"cocoartf1504\"

Backslash found where operator expected at write_mdp.pl line 2, near
"fonttbl\"

Backslash found where operator expected at write_mdp.pl line 2, near "f0\"

Backslash found where operator expected at write_mdp.pl line 2, near
"fmodern\"

Backslash found where operator expected at write_mdp.pl line 3, near
"red255\"

Backslash found where operator expected at write_mdp.pl line 3, near
"green255\"

Backslash found where operator expected at write_mdp.pl line 3, near "red0\"

Backslash found where operator expected at write_mdp.pl line 3, near
"green0\"

Bareword found where operator expected at write_mdp.pl line 4, near
"*\expandedcolortbl"

(Missing operator before expandedcolortbl?)

Backslash found where operator expected at write_mdp.pl line 4, near
"cssrgb\"

Backslash found where operator expected at write_mdp.pl line 4, near "c0\"

Backslash found where operator expected at write_mdp.pl line 4, near "c0\"

Backslash found where operator expected at write_mdp.pl line 5, near
"paperw11900\"

Backslash found where operator expected at write_mdp.pl line 5, near
"paperh16840\"

Backslash found where operator expected at write_mdp.pl line 5, near
"margl1440\"

Backslash found where operator expected at write_mdp.pl line 5, near
"margr1440\"

Backslash found where operator expected at write_mdp.pl line 5, near
"vieww10800\"

Backslash found where operator expected at write_mdp.pl line 5, near
"viewh8400\"

Backslash found where operator expected at write_mdp.pl line 6, near
"viewkind0

\"

(Missing semicolon on previous line?)

Backslash found where operator expected at write_mdp.pl line 7, near
"deftab720

\"

(Missing semicolon on previous line?)

Backslash found where operator expected at write_mdp.pl line 7, near "pard\"

Backslash found where operator expected at write_mdp.pl line 7, near
"pardeftab720\"

Backslash found where operator expected at write_mdp.pl line 7, near
"sl280\"

Backslash found where operator expected at write_mdp.pl line 9, near
"partightenfactor0


\"

(Missing semicolon on previous line?)

Backslash found where operator expected at write_mdp.pl line 9, near "f0\"

Backslash found where operator expected at write_mdp.pl line 9, near "fs24
\"

(Do you need to predeclare fs24?)

Backslash found where operator expected at write_mdp.pl line 9, near "cf2 \"

(Do you need to predeclare cf2?)

Backslash found where operator expected at write_mdp.pl line 9, near
"expnd0\"

Backslash found where operator expected at write_mdp.pl line 9, near
"expndtw0\"

Backslash found where operator expected at write_mdp.pl line 17, near ") \"

(Missing operator before \?)

Backslash found where operator expected at write_mdp.pl line 19, near "}\"

(Missing operator before \?)

syntax error at write_mdp.pl line 1, near "rtf1\"

syntax error at write_mdp.pl line 3, near "red255\"

syntax error at write_mdp.pl line 3, near "red0\"

syntax error at write_mdp.pl line 4, near "*\expandedcolortbl"

syntax error at write_mdp.pl line 4, near "cssrgb\"

syntax error at write_mdp.pl line 5, near "paperw11900\"

"use" not allowed in expression at write_mdp.pl line 12, at end of line

syntax error at write_mdp.pl line 17, near "unless"

syntax error at write_mdp.pl line 19, near "\}"

syntax error at write_mdp.pl line 31, near "for "

write_mdp.pl has too many errors.


Where am I going wrong? Looking forward to your kind help!

Regards,
Raag Saluja