[gmx-users] DNA podophyllotoxin

Paulo Netz paulo.netz at gmail.com
Fri Mar 30 18:38:45 CEST 2012

DNA simulations are very sensitive to force field, topology and simulation
protocols. In order to find out why this aggregation happened, some
is needed, such as how big was the DNA fragment, how were calculated
the long-ranged electrostatic interactions... From your post I assume that
acpype was used to generate the polophyllotoxin topology, but not the
DNA topology, right? I ask this question because the
DNA topology is easily constructed directly with pdb2gmx,
considering that the nucleotides already appear as building blocks
in GROMACS. If this was not the case, consider rebuilding the whole
system, because I don't know if acpype parameters are reliable to
use in DNA molecules. Besides that, 2.8 ns is too short to obtain
anything meaningfull in DNA simulations.

Best regards

Paulo A. Netz,
Instituto de Química,
UFRGS, Porto Alegre, Brazil

2012/3/30 Hovakim Grabski <hovakim_grabski at yahoo.com>

> Dear Gromacs users,
> I set up a simulation between the  DNA fragment and 6 podophyllotoxin
> molecules,  the topology files were generated with acpype,  simulation time
> was 2.8 nanoseconds, but the results are not what I expected. 4 molecules
> of PTOX formed an aggregate and then formed hydrogen bonds with the end of
> the DNA molecule. Could this happen because of the topology file?
> Thanks in advance
> Hovakim Grabski
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