Hello,
While converting parm and crd files with Amber atom types into sybyl mol2,
a "p5" atom (present in small organic molecule phosphates) is converted to
"C.3" in the mol2.
This conversion is happening in the program ambpdb, but it appears the
former top2mol2 program also results in the same.
I was able to trace this down to a definition in:
~dat/antechamber/ATOMTYPE_CHECK.TAB
Where p5 is mapped to C.3. All other phosphorus atom types are defined as
P.3. This also seems to be in conflict with this other file:
~dat/antechamber/CORR_NAME_TYPE.DAT
Where p5 seems to be defined as P.3 as far as I can tell.
When I change the definition in ATOMTYPE_CHECK.TAB to p5 P.3 I get the
expected outcome when converting the mol2, so this is definitely the file
ambpdb is reading in.
This same set of definitions is present in Amber16 to Amber22. I am
wondering if this is a mistake, or is there a reason for this? Thank you.
Regards,
--
Christopher Corbo
Ph.D. Student
Department of Biochemistry and Structural Biology
Member of the Rizzo Lab
Stony Brook University
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Received on Mon Apr 03 2023 - 11:00:03 PDT
