[gmx-users] simulation of mixed enantiomers

Justin A. Lemkul jalemkul at vt.edu
Fri Oct 10 22:00:48 CEST 2008

Anthony Costa wrote:
> 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.

Probably the parameters you are applying the enantiomers are either uniform, or 
inconsistent.  In other words, some R molecules are taking S parameters, and 
some are taking R parameters, and the same for the S molecules.

The easiest way to deal with this (as I have done in the case of mixed bilayers) 
is to place everything in the same order, in both the .top and the .gro.  For 
example, say you have two topologies - r.itp and s.itp - that you apply to the R 
and S molecules, respectively.  In the .top, you would:

#include "r.itp"
#include "s.itp"

In the [molecules] section, you would have to have:

R	x
S	x

...where 'x' is the number of each molecule type.  If different parameters are 
being applied, they cannot be grouped, which I think is what you are doing.

In the .gro file, all the R molecules would then have to appear before the S 
molecules.  If this is not the case with your .gro, it can easily be fixed using 
standard Unix tools like grep and cat.

> 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

Also probably from the inconsistencies I described above.

> 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
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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