[AMBER] ff_amber_to_viparr.py Error

From: iraklis litinas <iraklis.litinas.gmail.com>
Date: Sat, 4 Apr 2020 12:04:58 +0300

Hi Amber users.

 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
ff_amber_to_viparr.py 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)

Since now

1. I have checked the AC and the prepi files, to be sure that the numbering
and the names of all the atoms in my ligand are unique.

 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

3. I have checked the atomic numbers and the bonds between the atoms of the

4. In the following command

$SCHRODINGER/run -FROM desmond ff_amber_to_viparr.py -p gaff.dat -t
ligand.prepin AK1 -f ligand_antechamber

I added

-p ligand.frcmod because additional parameters are included there.

I still get the same error message. I would appreciate any good idea or

AMBER mailing list
Received on Sat Apr 04 2020 - 02:30:01 PDT
Custom Search