So did you visualize the simulation where you set ntwx=1 to see what was
actually happening? You will need to be prepared to do some detective work
here to figure out what is going on. A few things I note though:
> 1 N1 2.6080 0.8840 2.3780 n 1 MOL
>0.0000
> 2 C1 4.0750 0.7660 2.2570 c3 1 MOL
>0.0000
None of your atoms have any charges - this is probably the origin of the
problem and suggests something went wrong in the parameterization / charge
derivation step. I assume you used antechamber - it probably produced some
errors which were skipped.
> -------------------------------------------------------
> Amber 8 SANDER Scripps/UCSF 2004
> -------------------------------------------------------
This is a VERY old version of AMBER. I am assuming you applied all the bug
fixes from the website. Note though that this version is no longer
supported so there may be other bugs that aren't fixed.
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 1.4025E+05 2.6515E+04 1.2747E+06 O 173
>
> BOND = 45.5737 ANGLE = 46.7005 DIHED =
>169.9757
> VDWAALS = 146390.9270 EEL = -6438.2939 HBOND =
>0.0000
> 1-4 VDW = 31.5098 1-4 EEL = 0.0000 RESTRAINT =
>0.0000
Note your 1-4 EEL is zero here - this confirms my suspicion that the only
atoms in your system that have charges are the waters (which have no 1-4
term). This is what you will need to address to get your simulations
running correctly. I suggest working through the following tutorial using
AmberTools 12 - which you can download for free from the ambermd website.
http://ambermd.org/tutorials/basic/tutorial4b/
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Fri Nov 02 2012 - 09:30:03 PDT
