[AMBER] MMPBSA bad atom type error persisting

From: Kenneth Huang <kennethneltharion.gmail.com>
Date: Mon, 7 Dec 2015 13:40:13 -0500

Dear all,

I'm running into an odd situation where I'm hitting a bad atom type error
for K+ with MMPBSA.py.MPI in AmberTools15 on a remote cluster compiled with
Intel compilers, even after making the relevant changes to mdread2.f90 as-

         else if (atomicnumber .eq. 12) then
            ! Mg radius = 0.99A: ref. 21 in J. Chem. Phys.
1997, 107, 5422
            ! Mg radius = 1.18A: ref. 30 in J. Chem. Phys.
1997, 107, 5422
            ! Mg radius = 1.45A: Aqvist 1992
            x(L165-1+i) = 1.18d0 + 1.4d0
! Begin modification- add K+ atom type
         else if (atype == 'K+') then
            x(L165-1+i) = 1.52d0 + 1.4d0
! End modifications
            write( 0,* ) 'bad atom type: ',atype,' cannot perform SASA

I've already recompiled AmberTools in serial and parallel after making the
changes, but the error keeps persisting so I'm a bit at a loss- is there
somewhere else I should be adding in the atom type?

The only other change I've made is to the top line of MMPBSA.py.MPI at-


To this line-

#!/usr/bin/env python

Since MMPBSA.py.MPI wasn't playing nicely with the installed version of
python on the cluster (2.7) to get it to properly run.



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Received on Mon Dec 07 2015 - 11:00:03 PST
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