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Feature #720

permit pdb2gmx to choose a kind of HIS based on proton position

Added by David van der Spoel over 8 years ago. Updated almost 3 years ago.

Status:
Accepted
Priority:
Low
Assignee:
-
Category:
preprocessing (pdb2gmx,grompp)
Target version:
Difficulty:
simple
Close

Description

In release-4-5-patches and most likely all other pdb2gmx variants the hydrogens are ignored for selecting the HIS type.
The attached peptide may be used for testing:
pdb2gmx -f hid.pdb -ff amber99sb -water tip3p
will crash due to non-existence of HE2 while HD1 is present.

hid.pdb (2.88 KB) hid.pdb Gly-HisD-Gly peptide David van der Spoel, 03/13/2011 02:09 PM

History

#1 Updated by Rossen Apostolov over 8 years ago

  • Target version changed from 4.5.4 to 4.5.5

#2 Updated by Rossen Apostolov about 8 years ago

  • Target version changed from 4.5.5 to 4.5.6

#3 Updated by Berk Hess over 7 years ago

  • Status changed from New to Feedback wanted

With 4.5.5 I get:
Fatal error:
Atom HD1 in residue HIS 23 was not found in rtp entry HIE with 17 atoms
while sorting atoms.

This is a correct error message right?

Could you check again with 4.5.5?

#4 Updated by David van der Spoel over 7 years ago

Just recompiled the release-4-5-patches tree and error is still there.

#5 Updated by Rossen Apostolov over 7 years ago

  • Priority changed from Normal to High

#6 Updated by Rossen Apostolov over 7 years ago

With the latest 4-5-patches:

@Program pdb2gmx, VERSION 4.5.5-dev-20120411-66c78
Source code file: /home/rossen/Gromacs-dev/gromacs/src/kernel/pdb2gmx.c, line: 655

Fatal error:
Atom HD1 in residue HIS 23 was not found in rtp entry HIE with 17 atoms
while sorting atoms.
@

So we can close it, right?

#7 Updated by David van der Spoel over 7 years ago

Nope. For this peptide pdb2gmx should decide that it is a HID residue, not a HIE. If you add -ignh it can do what it likes. For structures from NMR that need to be pdb2gmx-ed while keeping the hydrogens this will cause serious problems. 10% of the HIS residues are HID in solution, in proteins I don't know the statistics.

#8 Updated by Berk Hess over 7 years ago

  • Category set to preprocessing (pdb2gmx,grompp)
  • Priority changed from High to Normal
  • Target version changed from 4.5.6 to 4.6

It seems that this issue is now more of a feature request than a real bug. pdb2gmx decided the protonation state of His based on the environment, not based on the actual protons, if they are present. The pdb file can be processed as you want using pdb2gmx -his
It would be nice to decide state based on the actual protons, but this is not a very common case. So someone interested in this should add this feature.

#9 Updated by Rossen Apostolov over 7 years ago

  • Tracker changed from Bug to Feature

#10 Updated by Erik Lindahl almost 7 years ago

  • Priority changed from Normal to Low
  • Target version changed from 4.6 to 5.0

Nice feature to have at some point, but not for 4.6. As Berk commented, that functionality is already possible by using the "-his" flag. Changing target to 5.0.

#11 Updated by Rossen Apostolov almost 6 years ago

  • Target version changed from 5.0 to 5.x

this won't be in 5.0. Keeping it open in case someone is interested in implementing it eventually.

#12 Updated by Mark Abraham about 4 years ago

  • Target version changed from 5.x to future

#13 Updated by Mark Abraham almost 3 years ago

  • Subject changed from pdb2gmx ignores hydrogens when selecting HIS to permit pdb2gmx to choose a kind of HIS based on proton position
  • Status changed from Feedback wanted to Accepted
  • Assignee deleted (David van der Spoel)
  • Difficulty simple added
  • Difficulty deleted (uncategorized)

Updated to reflect status

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