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
This e-mail and any attachments are only for the use of the intended recipient and may contain material that is confidential, privileged and/or protected by the Official Secrets Act. If you are not the intended recipient, please delete it or notify the sender immediately. Please do not copy or use it for any purpose or disclose the contents to any other person.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 11 2024 - 01:30:02 PDT
