Re: [AMBER] adding hydrogen to pdbqt ligand files

From: David A Case <>
Date: Tue, 28 Apr 2020 19:40:40 -0400

On Tue, Apr 28, 2020, Marawan Hussien wrote:

> Is there is a standard leap command to add hydrogen atoms to non-polar
> atoms (carbons) only during system building?

Leap is mainly just a bookkeeping program. It loads your units (e.g.
amino acids, nucleoctides, ligands that you many have defined.) The
hydrogens in the loaded units are the ones that will end up in the
prmtop file. Whatever tautomers or protonation states are in the unit
library file are the ones that will be used.

Put another way, leap knows almost nothing about chemistry. It is
simply comparing what is in the PDB file you load with unit definitions
you have already loaded.

If hydrogens are missing from a PDB you load (via loadPdb), the leap
will build those in, using internal coordinates stored in the unit
definitions. It has no logic to think about whether these hydrogens are
bonded to carbons or not.

....hope this helps.....dac

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Received on Tue Apr 28 2020 - 17:00:02 PDT
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