I am trying to parameterize a bimetallic Cd2+ using MCPB. I have obtained
all the required parameters for my system (these are attached). I am trying
to minimize the system but I am running into many problems. First, I am
attempting minimization of the water molecule around my system. However,
after several attempts, the minimization is failing at the start of
conjugate gradient minimization (my minwat.inp input file is also). The
following is a step-by-step procedure of what I did:
1) obtain parameters for Cd2+ and its ligands using MCPB (these are attached
1JGM_CD_sem.frcmod and 1JGM_CD_chg1.prep) - Note: i have modified these
several times to probe where the problem may be arising from
2) use the attached "leap.in" file with tleap to obtain the prmtop and
inpcrd files
3) run the minimization of the water molecules by restraining the rest of
the system.
the output file from the minimization just abruptly stops at NSTEP=500 which
is when Conj. Grad. minimization is to start. I have also attached the
output file as well.
I am getting a problem with 1-4 EEL = ************* being too large. I
thought that there may be some overlap problems with my initial system, but
this is not the case (or at least it's not now).
4) I have also attempted a gas phase minimization of my system, and at
NSTEP=500, the minimization also stops and I am getting the following error:
Frac coord min, max: -1152535.658565017 1152536.748611364
The system has extended beyond
the extent of the virtual box.
Restarting sander will recalculate
a new virtual box with 30 Angstroms
extra on each side, if there is a
restart file for this configuration.
SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
Atom out of bounds. If a restart has been written,
restarting should resolve the error
I would really appreciate some feedback on these problems. Note also that I
am having similar problems with using Mn2+ as the metal as well, but these
are when I heat my system
Thanks.
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- application/octet-stream attachment: leap.in
Received on Fri Aug 26 2011 - 08:00:03 PDT
