Hi Sathyaseenlan,
AMBER has the ion parameters for La3+, Pr3+, Ce3+, and Cl- ions.
I believe you can do that (solvate the DNA system with salt solution) through the following commands (herein I assume you are using the TIP3P water model):
source [leaprc file for a DNA force field]
source leaprc.water.tip3p
mol = loadpdb [pdb file name]
solvatebox mol TIP3PBOX 10
addions mol LA [number of La3+]
addions mol Cl- [number of Cl-]
The unit name of La3+ is LA (that is why you have “LA” in the fifth line), unit name of Pr3+ is PR, unit name of Ce3+ is CE or Ce, unit name of Cl- is CL or Cl-. You can found these information in the $AMBERHOME/dat/leap/lib/atomic_ions.lib file.
-Pengfei
> On Jul 16, 2019, at 6:14 AM, Satyaseelan C <bo17resch11006.iith.ac.in> wrote:
>
> 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
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> --
> *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*
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 14 2019 - 19:30:02 PDT
