I am constructing prepi and frcmod files from a PubChem 3D sdf file for a positively-charged (+1) S enantiomer. I do this by running antechamber and parmchk2:
antechamber -fi sdf -i compound.sdf -fo prepi -o compound.prepi -nc 1 -seq y -j 5 -rn LIG -c bcc
parmchk2 -f prepi -i compound.prepi -o compound.frcmod
I have a nice clean PDB structure in which there are two occurences of the heavy atoms of LIG.
When I run this through tLEaP, one LIG is S and the other is R (after using ambpdb for generating PDB from saved .prmtop and .crd files).
Is there an explanation for this behavior, as it is repeatable; and I'm not doing anything at all to the compound.sdf file and only removed unwanted waters and the like from the PDB file from RCSB.
Thank you,
Todd Minehardt
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Received on Tue Sep 05 2023 - 14:00:02 PDT
