Dear Prof. David A Case
Thank you for your suggestion. I
didn't properly explained about my problem.
1) I want to dissolve(solvate) the DNA system with salts like cecl3, prcl3
and lacl3 like nacl
looking forward for your suggestion
Thanks & Regards
Sathyaseelan
On Mon, Jul 15, 2019 at 5:01 PM David A Case <david.case.rutgers.edu> wrote:
> 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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--
*Thanks & Regards*
*C .Sathyaseelan *
*PhD Research Scholar*
*C/o Dr. Thenmalarchelvi Rathinavelan*
*Molecular Biophysics Lab*
*Dept. of Biotechnology*
*Indian Institute of Technology (IIT)*
*Kandi, Hyderabad, Telangana - 502285*
*Ph.No 8300150807, 9659750301*
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Received on Tue Jul 16 2019 - 03:30:02 PDT
