Re: [AMBER] tleap seems Si atom as S ... I don't know why

From: David A Case <>
Date: Sat, 12 Dec 2020 21:50:50 -0500

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.


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Received on Sat Dec 12 2020 - 19:00:03 PST
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