AMBER users,
I'm trying to run a simulation of a benzamide guest in a beta-cyclodextrin host with the implicit
GBSA water model. I've been using the gaff force field (with bugfix 7 "GBSA calculations using
the GAFF force field give a 'bad atom type' error" applied). In the input file I'm using igb = 1 and
gbsa = 1. When I try to do an initial minimization or if I try md, I get only question marks for all
my energy terms. The input files I'm using for minimization and the output file I get are below:
minimization of guest1, implicit water solvent
&cntrl
imin = 1, irest = 0, iwrap = 1, ntpr = 10, ntx = 1, igb = 1, gbsa = 1,
maxcyc = 100, ncyc = 500, ntmin = 1, dx0 = 0.1, drms = 0.0001,
ntb = 0, ntf = 1, cut = 10.0, nsnb = 10, ntc = 1,
&end
representative output:
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
NSTEP ENERGY RMS GMAX NAME NUMBER
1 6.1447E+01 3.7538E+01 1.9301E+02 S16 28
BOND = 83.9909 ANGLE = 4.5039 DIHED = 0.0235
VDWAALS = 1.6710 EEL = 19.2856 EGB = -16.0109
1-4 VDW = 6.4571 1-4 EEL = -40.4250 RESTRAINT = 0.0000
ESURF = 1.9505
NSTEP ENERGY RMS GMAX NAME NUMBER
10 ????????????? ????????????? 0.0000E+00 C2 1
BOND = ????????????? ANGLE = ????????????? DIHED = ?????????????
VDWAALS = ????????????? EEL = ????????????? EGB = ?????????????
1-4 VDW = ????????????? 1-4 EEL = ????????????? RESTRAINT = 0.0000
ESURF = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
20 ????????????? ????????????? 0.0000E+00 C2 1
BOND = ????????????? ANGLE = ????????????? DIHED = ?????????????
VDWAALS = ????????????? EEL = ????????????? EGB = ?????????????
1-4 VDW = ????????????? 1-4 EEL = ????????????? RESTRAINT = 0.0000
ESURF = 0.0000
.......
Has anyone come across this problem before? I've also tried to run the simulation using the 99
force field and have the same problem. Any suggestions would be greatly appreciated.
Thanks in advance,
- Brian Northrop
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Received on Wed Jan 14 2004 - 15:53:08 PST
