[gmx-users] Hypericin interaction with DNA molecule

Justin A. Lemkul jalemkul at vt.edu
Tue Jan 31 00:41:55 CET 2012

Hovakim Grabski wrote:
> Dear Sir,
> I'm a novice user.
> I compiled Gromacs in single precision.
> I tried to set up a simulation between  Hypericin and the DNA molecule 
> and to see how they interact.
> I created the Hypericin molecule with MarvinSketch and exported to a pdb 
> file,then with Avogadro I set up both molecules ,so that they are on a 
> distance of 2-3 A and saved to a pdb file.
> With pdb2gmx generated DNA's topology file(amber99sb,amber94 forcefield) 
> and in the log file says that the total charge of the System is 
> -32.431e,later when I tried to create a neutral system it's not a total 
> 0,but -0.430.
> I would like  to ask ,how reliable are the results,if the charge is not 
> an integer  and  i'm running in  single precision mode?

This fractional charge suggests that the topology is incorrect.  You should look 
carefully to see where it arises.  You should not use the topology in its 
current form; the results will not be representative of a reliable model as it 
does not reflect physical reality.

> Later I added the hydrogen atoms and added a charge to the Hypericin 
> molecule with Chimera USCF and then generated topology files with acpype 
> script.
> Before running md ,i created an index file linking the DNA and Hypercin 
> into on tc-grps and ran the simulation for 1 ns. Is it enough or it 
> should  run longer?

I would suspect that after 1 ns, the system is barely equilibrated.  The length 
of time required will depend on what you want to study, but modern simulations 
are typically orders of magnitude longer to conduct sufficient sampling and do 
reliable statistical analysis.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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