remove duplicate amino-acid definitions
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?
#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
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.