Thanks for the answer! I will try it.
David A Case <david.case.rutgers.edu>, 13 Ara 2020 Paz, 05:51 tarihinde
şunu yazdı:
> On Sat, Dec 12, 2020, Erdem Yeler wrote:
>
> >I parameterized a molecule including Si atom but when I prepared a
> topology
> >file I saw that tleap put 16 instead of 14 as Si Atom number. It didn't
> >cause any problems in my simulation but should I change the "Si" symbol in
> >my Si.frcmod and Si.mol2 file?
>
> The standard leaprc files, like leaprc.gaff2, don't define any atom
> types for Si. It's not clear how you made your mol2 and frcmod file,
> perhaps by hand?
>
> You need to include a addAtomTypes command to tell tleap what sort of
> atom your silicons are, e.g.
>
> addAtomTypes P
> { "??" "Si" "sp3" }
> }
>
> where you need to substitute whatever atom type you used for silicon for
> the ?? above.
>
> ....dac
>
>
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Received on Thu Dec 17 2020 - 05:30:03 PST
