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
_______________________________________________
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
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
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
