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Bug #2049

remove duplicate amino-acid definitions

Added by Mark Abraham about 4 years ago. Updated almost 4 years ago.

Status:
Closed
Priority:
Normal
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Category:
core library
Target version:
Affected version - extra info:
many versions affected
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Description

Some force field implementations apparently have copy-pasted definitions for amino acids with names that are synonyms (e.g. HIS1 and HISD in oplsaa). These should be removed in favour of some kind of symbolic reference.

Is xlateat.dat usable for this?


Subtasks

Bug #2047: Inconsistency for HISD charges for OPLS-AA/LClosedMark Abraham

Associated revisions

Revision 01f25ad5 (diff)
Added by Mark Abraham about 4 years ago

Removed HIS1 from oplsaa and charmm definitions

HIS1 is intended for linking with heme, which oplsaa doesn't
define. charmm converts HIS1 to HSD in its .r2b.

This makes the recent fix for oplsaa HISD "consistent" with HIS1.

Fixes #2047
Refs #2049

Change-Id: Ibc0463c779e76689dc7ef65e48aedc716de9e032

History

#1 Updated by David van der Spoel about 4 years ago

Not sure we want to "automate" this kind of transitions from something that was wrong to something that is fine by putting stuff in xlateat.dat. Just removing it should be fine, except for the fact that HIS1 is used to bind to HEME groups. Now these exist in GROMOS and CHARMM. In CHARMM it is translated to HSD automatically in the .r2b file:
; rtp residue to rtp building block table
;GMX Force-field
HISD HSD
HIS1 HSD
HISE HSE
HISH HSP

That is, if pdb2gmx detects a HIS bound to a HEME it will make it into a HSD. If I read these files right then we should not add something like this for force fields that have not been parameterized explicitly for HEME groups. In other words, HIS1 can go for everything except the GROMOS varieties and CHARMM.

#2 Updated by Berk Hess about 4 years ago

There is not even a heme building block in our oplsaa files, right?

I agree with David that we should remove them except for GROMOS.

#3 Updated by Berk Hess about 4 years ago

  • Status changed from New to Resolved
  • Assignee set to Mark Abraham
  • Target version set to 5.1.4

#4 Updated by Mark Abraham almost 4 years ago

  • Status changed from Resolved to Closed

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