[gmx-users] topolgen

farial tavakoli farial.tavakoli at ymail.com
Wed Jul 11 10:43:47 CEST 2018

Dear gromacs users
I am trying to run a simulation on my complex which has small molecule as a ligand , using OPLSAA ff. so I downloaded the topolgen-1.1.tgz and then installed perl script on linux. then typed "perl -v" to check if it is installed. the perl 5.20.1 is installed. 
but when I typed " perl topolgen.pl -f input.pdb -o output.top [-type itp/top] " command to generate ligand topology , faced with this error:
Can't open perl script "topolgen.pl": No such file or directory
Is there anyone to  help me to figure out this problem? 
Infact I am new user in generation topology for small molecules using OPLSAA ff. 


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