On Fri, Nov 11, 2011, Crystal.CHIA-YU Ku wrote:
>
> xleap seems like not to recognize Mg2+ ions, and my ligand TPS.
>
> Total number of electrons: 179; net charge: 0
> Please check the total charge (-nc flag) and spin multiplicity (-m flag)
Antechamber only works for closed shell molecules. Two things to check:
1. Does your ligand have a net charge? If so, you need to use the "-nc" flag
to antechamber to tell the program the total charge of the ligand, since the
default value is zero.
2. If that doesn't help, double check the input structure carefully. Make
sure all hydrogen atoms are present, and that the structure is consistent with
a closed shell neutral molecule.
Amber doesn't really have any default Mg2+ ion parameters. For a workaround,
check this link: http://archive.ambermd.org/201111/0020.html
....good luck....dac
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Received on Fri Nov 11 2011 - 15:30:03 PST
