[gmx-users] Regarding topology generation by using topologen_1.1.pl script

Justin Lemkul jalemkul at vt.edu
Tue Oct 24 19:20:33 CEST 2017

On 10/24/17 1:11 PM, Dilip H N wrote:
> Hello,
> I want to create a topology file for ammonia molecule and run using oplsaa
> FF. since ammonia molecule is not there in oplsaa FF, i created the
> molecule in Avogadro software and saved it as .pdb format. Then using the
> topolgen_1.1.pl pearl script (script by Justin Lemkul), i generated the
> topology. But the net charge on the molecule is 0.18 (for one molecule of
> ammonia).

TopolGen makes no attempt to intelligently parametrize any molecule; it 
makes guesses based on analogy to known molecules, and sometimes fails.

In fairness, the script does print out a really clear warning:

"Output topology has been written. An attempt has been made to assign 
charges and atom types based
on existing functional groups, but they may not be correct.  No charge 
calculations or other
parameterization calculations have been done.  Guesses have been made 
for charge groups.  Please
inspect and correct the topology before using it in any simulations.  
The author of the script does
NOT guarantee accuracy or usability of any of the content; TopolGen was 
written as a convenience
for outputting a skeleton topology, and nothing more."

> 1] So how do i neutralize the net charge (because it is difficult to add a
> non-integer charge), and hence carry out the simulation as neutral
> system..??

You don't. You can't use a topology with fractional charge.

> 2] Or is it possible to run by other scripts like mktop, acpype etc..??

Possibly. Try them.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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