[gmx-users] dna-ligand simulation
jalemkul at vt.edu
Thu Jan 17 11:36:42 CET 2013
On 1/17/13 1:19 AM, sarah k wrote:
> Dear all,
> 1- I’m trying to simulate a DNA-ligand complex. I have to use AMBER force
> field for the DNA structure. I have used PRODRG to get the required files
> and parameters of my ligand. PRODRG generates GROMOS based files.
> Consequently, when I add the ligand to my ligand topology and coordinates
> to DNA files, Gromacs can’t recognize some atom types in AMBER force field.
> Can I expect such simulation to give reliable results? How can I solve the
No, the result would be nonsense even if you managed to hack the topology into
working. Do not mix and match force fields. You will need to find a way to
generate ligand parameters that are compatible with the AMBER force field you've
chosen (acpype, antechamber, etc).
> 2- I would like to save my final *.gro file during md simulation step
> after each 0.5 ns. How can I do so?
The simplest way is to set an appropriate value of nstxtcout and use trjconv to
extract the frames later.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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