[gmx-users] dna-ligand simulation

Justin Lemkul 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
> problem?

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.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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