The topologies should not be identical, surely? Check out the section on improper dihedrals in the manual, it's possible to specify an improper to keep enantiomers in their intended handedness.
----- Original Message ---- From: Anthony Costa <[EMAIL PROTECTED]> To: [email protected] Sent: Friday, October 10, 2008 8:45:55 PM Subject: [gmx-users] simulation of mixed enantiomers i have a simulation where i would like to study the interaction of N small molecules of various enantiomeric composition. if i use a simple R+S situation (N=2) by inserting the other enantiomer into my already created box, subsequent minimization either yields unphysical structures for the inserted enantiomer or will often reverse its symmetry to that of the original molecule. i am clearly missing something about the configuration of a reasonable topology for this type of system, but i'm can't quite figure it out. not surprisingly, i get errors when creating the mdp file for my energy minimization. the topologies created for both R and S enantiomers are identical, as i would expect (in this case they are small amino acid residues), when created individually, so i usually just increment the number of molecules in my original topology file after inserting the opposite enantiomer. WARNING 1 [file "topol.top", line 159]: 13 non-matching atom names atom names from topol.top will be used atom names from 2_2mer.gro will be ignored what am i missing? thanks for your time, anthony -- Anthony B. Costa Purdue University Department of Chemistry 560 Oval Drive, #365 West Lafayette, IN 47907 _______________________________________________ gmx-users mailing list [email protected] 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 _______________________________________________ gmx-users mailing list [email protected] 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
