Hi,
I think you will check your format of input PDB files carefulling. You can learn sth. from checking from Leap.
Good luck!
Wu YL
======= 2003-12-11 23:28:00 您在来信中写道：=======
>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
