Marc, > 1. Generated a two molecule complex and saved as .pdb > 2. Parsed the file out to retain relative coordinates > of each molecule in separate .pdb files > 3. Run both resulting molecules through PRODRG server > to generate .gro files for GMX processing.
FYI, you can use the editconf script to convert a pdb file to gro. Did you visualise the molecules at this point? > 4. Merge molecules back together into a single complex > .gro file (again, hoping the coordinates are > preserved) If you see things all messed up at this point, with them fine before merging, then as Erik noted, you have messed up the gro file format when merging the two molecules into one file. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
