[gmx-users] How to define ligand / metal atoms in gbsa.itp file of a force field for implicit MD??

[Mark Abraham]

Hi,

On Mon, Mar 12, 2018 at 10:11 AM Vishwambhar Bhandare <vishwayogi at gmail.com>
wrote:

> Dear users,
>
> I want to perform implicit simulation for a protein-ligand complex.
> for a protein alone, implicit works fine, but for ligand atoms it shows
> error as copied below,
>
> Setting gen_seed to -1914387900
> Velocities were taken from a Maxwell distribution at 300 K
> GB parameter(s) missing or negative for atom type 'N3'
> GB parameter(s) missing or negative for atom type 'H'
> GB parameter(s) missing or negative for atom type 'CT'
> GB parameter(s) missing or negative for atom type 'HP'
> GB parameter(s) missing or negative for atom type 'HC'
> GB parameter(s) missing or negative for atom type 'H1'
> GB parameter(s) missing or negative for atom type 'S'
> GB parameter(s) missing or negative for atom type 'C'
> GB parameter(s) missing or negative for atom type 'O'
> GB parameter(s) missing or negative for atom type 'OH'
> GB parameter(s) missing or negative for atom type 'HO'
> GB parameter(s) missing or negative for atom type 'H5'
> GB parameter(s) missing or negative for atom type 'H4'
> GB parameter(s) missing or negative for atom type 'HA'
> GB parameter(s) missing or negative for atom type 'MG'
> GB parameter(s) missing or negative for atom type 'P'
> GB parameter(s) missing or negative for atom type 'OS'
> GB parameter(s) missing or negative for atom type 'H2'
> GB parameter(s) missing or negative for atom type 'c1'
>
> Program: gmx grompp, version 2016.4
>
> Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1296)
> Fatal error:
> Can't do GB electrostatics; the implicit_genborn_params section of the
> forcefield is missing parameters for 19 atomtypes or they might be
> negative.
>
>
> How can I get the parameters defined in gbsa.itp file..???
>

The general answer to this is "develop the parameters using a method
consistent with the way the rest of the parameters were developed" which
generally means you need to read and understand how those were developed,
and use the same tools to fill gaps. In many cases you can probably define
radii by analogy between the atom types, and how buried the ligand is, but
that's a judgement you need to make as part of developing the description
of your system.

Mark


> --
> Dr. Vishwambhar Vishnu Bhandare
> Post Doctoral Fellow
> Department of Biosciences and Bioengineering
> Indian Institute of Technology
> Bombay-400076
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