[gmx-users] simulation of mixed enantiomers

Alan Dodd anoddlad at yahoo.com
Sat Oct 11 00:29:36 CEST 2008

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 <acosta at vdov.net>
To: gmx-users at gromacs.org
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 B. Costa
Purdue University
Department of Chemistry
560 Oval Drive, #365
West Lafayette, IN 47907
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