Re: [AMBER] Error

From: David A Case <>
Date: Sat, 4 Apr 2020 13:22:49 -0400

On Sat, Apr 04, 2020, iraklis litinas wrote:
> I am trying to simulate two complexes of the same protein, with two
>different ligands. The two ligands differ only in one atom. Both ligands
>have an aromatic thiophen ring, substituted with a bromine atom in the
>first one and with an iodine atom in the second one (on the same C atom). The
>two ligands were sketched with the 2D sketcher tool of Maestro (GUI of
>Desmond) and extracted as mol2 files. After docking the ligand in my
>protein and running the Protein Preparation Wizard for the protein-ligand
>complex, the desmond-out.cms was prepared.
> For the simulation I use the Amber99sb force field. In order to convert
>Amber topology and force – field files into Desmond format, I use the
> script. Viparr gives the amber-exe file and the
>simulation runs without a problem for the Br-ligand. But that is not the
>case for the I-ligand, for whom I encounter the following error message.
>Error: Struct 2, Res <" _INS_ ",900> (UNK) not matched by any force field
>template with formula C(15)H(21)I(1)N(1)S(1)

I'm guessing that very few people on this list will be familiar with the
workflow you are using, and you will probably have to check with
Schrodinger about problems.
> 2. I have checked the characterization of all the atoms of the ligand,
>contrasting AC, prepi, ligand- template and gaff.dat files. I changed the
>characterization for two hydrogen atoms because, it was obviously wrong
>(hydrogen bonded with a nitrogen atom was assigned as bonded with an sp3 C

This sounds rather concerning. Did you run antechamber to get the prepi
file? Or was it done with some schrodinger product? And where did the
ligand.frcmod file come from?

If you think there is a specific problem with Amber (say with
antechamber), please provide more details. But it sounds possible that
it is Viparr (or some other non-Amber tool) that is having problems with


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Received on Sat Apr 04 2020 - 10:30:02 PDT
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