> I run MD simulations for 100ns for a GAG-receptor-Mn complex. After
> running mmpbsa.py I am obtaining an error message:
>
> bad atom type: Mn
This comes from sander which hard codes parameters used for surface area
(mdread.F90). Mn is not coded into this... I do not know what parameters
I would choose to code in but would experiment noting that the likely
difference compared to Mg in surface area contributions will be modest
compared to differences in electrostatic components (free energy of
solvation) but I haven't look these up or calculated them.
An additional issue you will face is what are the effective radii for
generalized Born or PB calculations for both magnesium and Mn and whether
these in fact reproduce experimental solvation free energies. In the past,
when doing less standard ions we had to explicitly set radii to match free
energies of solvation from PB or GB calculations by hand or suffer from
inaccurate energies. As the manuals for MM-PBSA repeatedly stress, these
tools are block box and you should in an ideal world be able to do some of
these energetics by hand.
[To figure out where/what code these messages from come, egrep can be your
guide...]
--tec3
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Received on Wed Jun 20 2018 - 04:00:03 PDT
