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Bug #554

pdb2gmx is not compliant with PDB 3.2 Nomenclature

Added by Alan empty about 9 years ago. Updated about 9 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Erik Lindahl
Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

For example

wget -c "http://www.pdbe.org/download/1BVG" -O 1BVG.pdb
grep 'ATOM ' 1BVG.pdb>| Protein.pdb

pdb2gmx -ff amber99sb -f Protein.pdb -o Protein2.pdb -p Protein.top -water spce

[snip]
Fatal error:
Atom HB3 in residue PRO 1 not found in rtp entry NPRO with 16 atoms
while sorting atoms. Maybe different protonation state.
Remove this hydrogen or choose a different protonation state.
Option -ignh will ignore all hydrogens in the input.

I know this error very well and indeed -ignh would solve the problem.

What really does not feel good about pdb2gmx is that the 'pdb' part of its name doesn't honour it. I mean, I get a file from PDB, original and pdb2gmx only works if you ignore the H.

It's all about the fact the in the current PDB standard atom name nomenclature we have for, e.g., LEU HB2 and HB3 instead of HB1 and HB2 as pdb2gmx expects.

History

#1 Updated by Berk Hess about 9 years ago

There are two issue here.
Most force fields do not follow the HB2, HB3 nomenclature,
but use HB1, HB2. For 4.5 we went through a considerable amount
of effort to produce force field specific atom names.
So what we should have is a renaming scheme for every force field
that renames many hydrogens from the official scheme to the force field scheme.
We probably also need a good check to identify which naming scheme the input
pdb file uses.

This is too much work and changes for 4.5.?.
We'll fix this later.

Berk

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