Dear Amber mailing list,
I'm trying to set up a system with a protein that binds GTP and GDP nucleotides. However, the magnesium ions that coordinate the phosphate tails keep getting misplaced in the final system. I.e. they are nowhere close to the nucleotides even though the input PDB coordinates are correct (the output coordinates are somehow changed in the final system). I've attached my corresponding leap script for reference. If you need other files to troubleshoot this issue let me know, but since there are quite a few involved I won't send them right away in case it's something obvious in the leap script.
Thanks,
Andrew
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 18 2015 - 10:00:03 PDT
