[AMBER] Using fluorine and iodine in Antechamber

From: Pietro Aronica via AMBER <amber.ambermd.org>
Date: Tue, 11 Jun 2024 08:24:47 +0000

Dear all,
There is a minor oversight in antechamber that makes it hard to use fluorine and iodine atoms with certain names in antechamber. For example, I might name a fluorine atom FD1 in my pdb, to indicate that it is bonded to CD1, which is delta carbon 1; however, antechamber will interpret those FD characters literally, try to find element Fd, fail, and quit with this error:

Unrecognized case-sensitive atomic symbol ( FD1).

The only way to have it recognise it as a fluorine atom, is to change its name to only contain F and numbers, which is the workaround I have had to use. However, this is no longer possible for my code and I find myself needing to name an atom FX and have it read as a fluorine atom. The same issue is present for iodine.
I know this is possible because antechamber has no issue with recognising C, N, O, S and H atoms (all elements with one-character symbols) as carbon, nitrogen, oxygen, sulfur or hydrogen, even when the character is followed by an X. If I remember correctly, when I first encountered this error it was because there was an if statement somewhere within antechamber that parsed the atom name to determine the element and it had a provision to account for elements with one-character symbols but did not extend it to fluorine and iodine. I haven't been able to find again the same part of the code, however, and it may be a different cause.
This has been going on for years, as far as I can tell. There are others in the mailing list (here<http://archive.ambermd.org/202302/0088.html> for example) that have had the same issue. I recognise this is not major bug but it would be helpful if in a future update fluorine and iodine could be treated in the same way as other atoms with one-letter atomic symbols, that would be helpful.
Kind regards
Pietro Aronica
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Received on Tue Jun 11 2024 - 01:30:02 PDT
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