I forgot to mention that it put TER after every ion. The tleap program can
also identify the double strand of the DNA and accordingly put TER below
each DNA strand. Each single ion and water molecules are separated by TER.
Thanks.
Sunita
On Fri, Mar 27, 2020 at 8:49 AM Sunita Patel <sunita.patel.cbs.ac.in> wrote:
> 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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>>
>
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Received on Thu Mar 26 2020 - 20:30:03 PDT
