Re: [AMBER] ATOMIC NUMBER section in prmtop file - sulfur atom in ligand is -1?

From: David A Case via AMBER <>
Date: Mon, 5 Sep 2022 09:14:12 -0400

On Mon, Sep 05, 2022, He, Amy via AMBER wrote:

>One is the original prmtop I generated by Leap. In the ATOMIC NUMBER
>section, the ligand sulfur atom is -1.

I'm guessing(?) that you defined a new sulfur atom type for the ligand,
but neglected to have a addAtomTypes command in your tleap script:

addAtomTypes {
    { "xx" "S" "sp3" }

Where "xx" is your new atom type. Still, this should not make any
difference, since (I think!) Amber only really uses the atomic number for
QM/MM calculations, not for conventional force fields.

Also, the masses are irrelevant for minimization. I think we would need
to have files to reproduce the problem you are seeing (for a small test
case). It sounds like my assumption that the atomic number section is not
relevant is probably wrong.

You might be able to make some progress by looking the breakdown of energy
terms for the starting structure, using both prmtop files. Are all fields
the same except for the VDW term?

If you did leave out the addAtomTypes entry, you could try to fix that, then
regenerate the prmtop file with tleap. Maybe something else is different as
well. Use the parmed commands printLJTypes and printLJMatrix to examine
your nonbonded interactions. Look especially for things related to the
sulfur atom.

...good luck...dac

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Received on Mon Sep 05 2022 - 06:30:03 PDT
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