Dear gmx users I want to run the system by OPLS forcefield. My system has protein, water and 1 ligand (Boromohexane) and NA. At the first I put the protein in the water and minimized it then add the ligand to system. I already made a itp file for the ligand. I add the ligand itp file to the topology file which was include the itp file of protein and water and Na to nautral the system. But after running grompp i faced with the following ERRORR:
calling cpp... topol.top:43944:18: error: Br.itp: No such file or directory cpp exit code: 256 Tried to execute: 'cpp -I/usr/local/gromacs/share/top -DFLEXIBLE topol.top > grompp4OawMo' The 'cpp' command is defined in the .mdp file processing topology... Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 3 bonded neighbours for Protein 1 Excluding 2 bonded neighbours for SOL 11433 Excluding 1 bonded neighbours for NA+ 18 Cleaning up temporary file grompp4OawMo ------------------------------------------------------- Program grompp, VERSION 3.3.3 Source code file: toppush.c, line: 1396 Fatal error: No such moleculetype MOL As you see it says that Br.itp file does not exist in this directory which is not true. All of my files are in the same folder and I am confusing what should be wrong? thanks _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
