[gmx-users] dna-ligand simulation

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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