permit pdb2gmx to choose a kind of HIS based on proton position
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.
#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
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.
#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 (
Updated to reflect status