Dear Dac,
I checked it in AMBER 18. The tleap program itself puts TER statement at
the required places even if it is not present in the PDB file.
There is a good improvement. It was not there in AMBER 12.
Thanks a lot.
Sunita
On Thu, Mar 26, 2020 at 7:40 AM David A Case <david.case.rutgers.edu> wrote:
> On Thu, Mar 26, 2020, Sunita Patel wrote:
>
> >The "TER" statement is provided to separate the disconnected segments.
> > Do I need to provide TER statement to separate two Mg2+ ions?
> >
> >This is the end part of my PDB file. Is it fine or I need another TER
> >statement between two Mg2+ ions?
> >-------------------------------------------------
> >ATOM 485 OP1 DG3 147 -9.954 -7.989 10.887 1.00 0.00
> > O
> >ATOM 486 OP2 DG3 147 -8.081 -8.158 12.615 1.00 0.00
> > O
> >TER
> >HETATM 487 MG MG 148 -12.766 -5.036 -6.481 1.00 0.00
> > Mg
> >HETATM 488 MG MG 149 -10.500 9.645 5.380 1.00 0.00
> > Mg
> >END
> >--------------------------------------
>
> Can you not just try a quick experiment, and see what happens with or
> without the TER card?
>
> (Apologies for the abrupt tone: I'm teaching computational chemistry
> this semester, and trying to instill in my students a willingness to
> experiment. All Amber users, even very experienced ones, find things that
> they don't understand, or that the manual doesn't explain. Figuring out
> how to move forward is a key skill; cf. my previous post right before this
> one.)
>
> (Plus: I don't know the answer!)
>
> ...good luck...dac
>
>
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Received on Thu Mar 26 2020 - 20:30:02 PDT
