Your bond energy is not really that high since your system is relatively
large (~40,000 atoms, judging from "NUMBER", perhaps a lot more?). The
average bond energy per atom (or per bond, since TIP3P water has three
bonds) was about 0.5 kcal/mol (perhaps less) which looks reasonable to me
since you did not use SHAKE (in minimization). If bad (or fantastic) things
did happen, your EEL energy should be much lower (to ******) and you could
have found the simplest way to make a 13N which could have been a
price-winning work :).
Nevertheless, do check the AMBER web site about LINMIN failure.
Simple solution, reduce number of minization steps from 5000 to 200 (which
is my favorite number).
Simpler solution, don't worry.
But from what you posted, the minimization finished at 5000 steps and
everything looks great :).
Hope this helps.
yong
***********
Your bond energy is very high. You should check to see when that happens.
Use a google search or check the Amber web page to see about the LINMIN
message. If you are using any new parameters, make sure they can be
minimized ok without the water and PME first.
blakrose.gazeta.pl wrote:
>Dear Amber users!
>
>I have a problem with minimization. I'd like to minimize my complex in
>explicit water. After ncyc steps i get LINMIN FAILURE, besides my EEL
>is very small and I don't understand why. What should I do to make it
>ok?
>
>Here is my input:
>
>
> &cntrl
> imin=1, maxcyc=5000, ncyc=250,
> scee=1.2, cut=10., ntb=1,
> dielc=1.0,
> nsnb=20,
> ntpr=5,
> ntr=0,
> &end
> &ewald
> use_pme=0,
> nbflag=0,
> netfrc=0,
> eedmeth=1,
> &end
>
>
>AND SOME STEPS RESULTS:
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -3.3984E+05 4.1586E+01 1.6707E+02 O 37243
>
>
> BOND = 169.0292 ANGLE = 775.6756 DIHED =
>2442.9634
> VDWAALS = 15540.5997 EEL = -369563.2216 HBOND =
> 0.0000
> 1-4 VDW = 893.4733 1-4 EEL = 9904.0581 RESTRAINT =
> 0.0000
>
> NSTEP ENERGY RMS GMAX NAME
>NUMBER
> 5000 -4.3781E+05 2.5434E+01 1.0193E+02 O 30781
>
>
> BOND = 22641.7740 ANGLE = 834.7894 DIHED =
>2478.7620
> VDWAALS = 15853.8954 EEL = -490543.4151 HBOND =
> 0.0000
> 1-4 VDW = 900.7907 1-4 EEL = 10021.6052 RESTRAINT =
> 0.0000
>
>
>Please please help me.
>Thanks in advance.
>Pawel
>
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Received on Sat Aug 20 2005 - 14:53:01 PDT
