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

[Justin Lemkul]

On 3/23/18 2:54 AM, Raag Saluja wrote:
> 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

All of the errors point to some kind of rich-text formatting, meaning 
you corrupted the script or altered it in a non-plain-text editor. 
Download a new copy of the script and don't alter it.

-Justin

> 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

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================