Project

General

Profile

Bug #206

Protein atom naming in pdb files incorrect

Added by David van der Spoel over 11 years ago. Updated about 11 years ago.

Status:
Closed
Priority:
Normal
Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
Close

Description

The naming of protein atom names in pdb file by gromacs is incorrect. We are using e.g. HG12 and HE12 which means that the characters re shifted to the left in the pdb file columns. In many application this has the consequence that these atoms are interpreted as Mercury and Helium. Instead we should name the atoms 2HG1 and 2HE1 respectively, as many other applications do.

History

#1 Updated by Erik Lindahl about 11 years ago

Fixed in 4.0 branch.

Also available in: Atom PDF