[gmx-users] Hypericin interaction with DNA molecule

Hovakim Grabski hovakim_grabski at yahoo.com
Tue Jan 31 00:13:56 CET 2012

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?
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?
My PC is quadcore Q6600 with 2 gigs of ram.
Thanks in advance

Hovakim Grabski
Russian Armenian (Slavonic) University
Bionformatics Department
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