Quoting pkmukher <[EMAIL PROTECTED]>: > Hello users, > > I found a problem similar to one described in the mailing > list. The problem occurs in grompp wherein it says > unrecognized atom type CB. As suggested in the mailing list > the problem arises when in a ligand protein system the > ligand is prepared using the PRODRG server GROMOS87 format > and the protein is prepared in some other FF..in my case > 43a1(GROMOS96)..when i prepared my protein using the -ff gmx > flag (gmx Gromacs Forcefield (a modified GROMOS87)) grompp > did not have any problems. My question is that is there a > way to prepare the ligand in 43a1 format so that when i run > grompp the relevant input files are is the same desired > format. Thanks in advance
I believe the PRODRG beta server provides parameters compatible with Gromos96 43a1. -Justin ================== Justin A. Lemkul Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] (540) 231-9080 ================== _______________________________________________ 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
