On Mon, Jul 15, 2019, Satyaseelan C wrote:
> I want to do MD simulation for DNA with cecl3,
>lacl3 and prcl3 metals. I gone through couple of tutorials and articles
>for force field selection and adding force field parameters with existing
>force field, but i am unable to do it. I am requesting you give any
>suggestion or methodology to do MD simulation.
Amber would treat these as Ce+3 positive ion, plus Cl- negative ions
(etc). Ce3+ has atom/residue name of "CE"; La3+ is "LA"; Pr3+ is "PR";
Cl- is "CL".
You will have to hand-edit your input pdb file to use these atom and
residue names, if some other convention is being used. (But what is
shown above is the official PDB standard.)
...hope this helps....dac
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Received on Mon Jul 15 2019 - 05:00:02 PDT
