OK, thanks so much again!
For me its indeed very important to know the original water: in my
model I am focusing on Na+ coordinated site embedded within allosteric
pocket of the protein. The water here is fill the same pocket, thus
providing a screening effect for the ion.
We have simulated this system in n*md and the water surprisingly have
not been exchanged, being a very stable during 100 ns.
What are the general methodological approach to keep the water and ion
from the initial pdb?
As I have processed the structure to pdb2pqr (to assign pronation
states and convert residues to amber ff names) and then to pdb4amber
(Check a residue names and disulfide bonds), all hetatms from initial
pdb were disappeared. However I can copy the following part of pdb
from the original pdb before it processing via pdb2pqr:
HETATM 2412 NA NA 300 5.951 -3.628 -16.487 1.00 16.13 NA
HETATM 2413 O HOH 301 6.306 -7.096 -23.041 1.00 6.19 O
HETATM 2414 O HOH 302 2.071 -8.293 -17.027 1.00 10.42 O
HETATM 2415 O HOH 303 6.638 -2.849 -19.215 1.00 19.58 O
HETATM 2416 O HOH 304 6.117 -6.199 -17.892 1.00 10.13 O
HETATM 2417 O HOH 305 7.067 -6.908 -20.307 1.00 8.66 O
HETATM 2418 O HOH 306 6.999 2.679 -15.468 1.00 27.72 O
HETATM 2419 O HOH 307 5.105 -0.681 -18.772 1.00 16.73 O
END
should I rename the HOH to WAT and than add all of those records back
at the beginning of the post-processed pdb? What water model would be
better for this system (SPC or TIP3P?)
Gleb
2017-08-02 13:26 GMT+02:00 David A Case <dacase.chem.rutgers.edu>:
> On Wed, Aug 02, 2017, James Starlight wrote:
>>
>> 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?
>
> No: this is way outdated, deriving from days (still somewhat with us), when
> Amber developers thought they could just make up any atom and residue names
> that seemed to make sense. (Many Amber scripts accept "Na+" for backward
> compatibility, but you should not use that going forward.)
>
>>
>> 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).
>
> No: if you wish to keep track of the "original" waters (note that they will
> generally exchange with others rather quickly), you'll have to note their
> residue numbers (e.g. 303 to 309 in the above example.) (There are technical
> reasons inside the code for requiring all waters to have the same residue
> name. I don't think this is likely to change any time soon.)
>
> ...dac
>
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Received on Wed Aug 02 2017 - 07:00:03 PDT
