Dear David,
Thanks so much for the responce!
Here some additional questions:
1) Regarding Na+:
for the Amber format it shoud be like
ATOM 5020 Na+ Na+ P 302 2.736 1.538 0.711 0.00 0.00 NA+
right?
Because initially I obtained pdb from modeller where it was HETATM:
HETATM 2450 NA NA 302 -13.016 13.036 54.214 1.00 44.33 NA
2) is it possible to keep in the model the coordinates of X-ray water
which is in initial pdb was defined as:
HETATM 2451 O HOH 303 -18.411 13.587 59.094 1.00 27.41 O
HETATM 2452 O HOH 304 -11.894 17.279 58.575 1.00 18.35 O
HETATM 2453 O HOH 305 -15.811 12.728 54.157 1.00 39.81 O
HETATM 2454 O HOH 306 -13.656 13.200 56.969 1.00 30.52 O
HETATM 2455 O HOH 307 -15.863 12.568 58.351 1.00 29.97 O
HETATM 2456 O HOH 308 -13.880 11.747 48.007 1.00 24.15 O
HETATM 2457 O HOH 309 -15.865 14.129 51.849 1.00 32.31 O
After tleap processing I'd like to change it name indicating that it
is not solvent water (WAT).
3) For this kind of the system (with embedded Na) in cofactor site,
which model of water is better (TIP3P or SPC)?
Thanks so much !
James
2017-08-01 19:23 GMT+02:00 David A Case <dacase.chem.rutgers.edu>:
> On Tue, Aug 01, 2017, James Starlight wrote:
>>
>> I need to include in a model a metal cofactor (Na+ ion) embedded
>> within an allosteric pocket on the protein. Here I would like to
>> parametrize the ion as non-bonded model.
>>
>> Assuming that I know the position of the NA from a given pdb, which
>> parametres should I use for tleap for the parametrisation of the
>> complex and how I should name NA within the input pdb?
>
> NA ions are standard in Amber, and get loaded along with the corresponding
> water models in the leaprc.water.* files. You should follow the PDB standard,
> and name both the atom and the residue as NA in your input pdb file.
>
> ...dac
>
>
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Received on Wed Aug 02 2017 - 04:00:02 PDT
