[AMBER] Mg 12-6-4 potential using parmed

From: Brian Radak <radak004.umn.edu>
Date: Thu, 28 Aug 2014 15:45:19 -0400

I have a simple prmtop file for an RNA system with a bound Mg that I want
to convert from a normal 12-6 to the new 12-6-4 potential. I tried using
the following parmed.py commands:

>>parmed.py prmtop
add12_6_4 :MG watermodel TIP4PEW

and got the following error/warning:

Adding Lennard-Jones C-coefficient for 12-6-4 potential. Polarizabilities
read from
Using default C4 parameters for water model [TIP4PEW].
The selected metal ion is Mg
Action add12_6_4 failed
    LJ12_6_4Error: Could not find parameters for ATOM_TYPE CS

So I tried modifying "lj_1264_pol.dat" by adding the CS type. Presumably
this was omitted because CS and Cs could cause trouble (so I also deleted
the Cs line because I don't really need that for now)? In any event I now
get this error:

The selected metal ion is Mg
Traceback (most recent call last):
  File "/home/radakb/devel/git/Programs/Amber11/bin/parmed.py", line 161,
in <module>
  File "/usr/lib64/python2.7/cmd.py", line 142, in cmdloop
    stop = self.onecmd(line)
  File "/usr/lib64/python2.7/cmd.py", line 221, in onecmd
    return func(arg)
  File "<string>", line 1, in <lambda>
line 141, in _normaldo
line 2857, in execute
  File "/u2/home2/radakb2/git/Programs/Amber11/bin/ParmedTools/add1264.py",
line 119, in params1264
    atomtypej = amberatomtypelist2[j]
IndexError: list index out of range

Which is a bit more opaque to me. Any ideas?


================================ Current Address =======================
 Brian Radak                                            :     BioMaPS
Institute for Quantitative Biology
 PhD candidate - York Research Group       :     Rutgers, The State
University of New Jersey
 University of Minnesota - Twin Cities          :     Center for
Integrative Proteomics Room 308
 Graduate Program in Chemical Physics     :     174 Frelinghuysen Road,
 Department of Chemistry                          :     Piscataway, NJ
 radak004.umn.edu                                 :
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Received on Thu Aug 28 2014 - 13:00:03 PDT
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