> And what is my current issue is? What should I replace the residue name with?
Ultimately, what ever you want to. From the name of the file, it seems like it is formaldehyde, which is a small molecule, and from the link I provide you the residue name used for it is FLH. So, convention wise, that is probably the best name to use for it. But, that is not going to solve your problem, since you are attempting to use pdb2gmx to generate your topology. And that is not going to work because FLH will not be in the residue database, as is noted at the link that was provided to you (http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in _residue_topology_database) I would suggest you actually READ what is at URL above. Funny enough, on the second line it actually mentions formaldehyde, take note of what it actually says. Plus also take notice of the second paragraph. 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 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
