Re: [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

--


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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[gmx-users] DNA-ligand simulation with AMBER FF

[Paulo Netz]

Dear Gromacs Users


I am simulating the interactions between ligands and DNA
using GROMACS with the AMBER force field, as implemented with
the AMBER PORT for GROMACS. Simulating DNA is actually
very easy with this protocol, but for the ligand some
problems arise. Until now we are constructing the
topology manually, but this became complicated for large
ligands. What is the best way to construct ligand
topologies with AMBER parameters, for using with GROMACS,
provided that we DO NOT have the AMBER package?

Thank you very much in advance.

Paulo Netz
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