Thank you very much for your help.
I'm going to try to use XMIN instead of the standard minimizer but i will get now an error
ERROR in load_lbfgs(): YS=0
some ideas???
Best reagrds
Jan Wahl
Am 11.01.2011 um 16:05 schrieb Jason Swails:
> Hello,
>
> This is a very common error that has been widely discussed in the past (look
> through the amber mailing archives). In fact, there was even a webpage
> devoted to it: http://ambermd.org/Questions/linmin.html.
>
> Basically, the standard amber minimizer is not good enough to do the type of
> minimization you're asking it to do, since it got caught in a spot it
> couldn't find its way out of. If you want to do a better minimization,
> consider using XMIN (see the ntmin variable description in the amber
> manual).
>
> Good luck!
> Jason
>
> On Tue, Jan 11, 2011 at 8:11 AM, Jan Wahl <JanWahl.gmx.de> wrote:
>
>> Dear community,
>> i have a strange problem doing a conformation analysis using a python
>> script and amber 11. I'm doing some minimizations using the following
>> sander-input
>>
>>
>> # Running minimization
>> cat << eof > min.in
>> # 200000 steps of minimization
>> &cntrl
>> maxcyc=200000, imin=1, cut=12.0, igb=1, ntb=0, ntpr=10,
>> /
>>
>>
>>
>>
>>
>> sander is started usuing the following commands
>>
>> sander -O -i sander.in -o out.out -p prmtop -c inpcrd
>>
>>
>>
>> in the following you can see the end of my outputfile
>>
>>
>> NSTEP ENERGY RMS GMAX NAME NUMBER
>> 34000 -8.1184E+01 9.1854E-04 3.4484E-03 C4 54
>>
>> BOND = 2.1401 ANGLE = 20.5820 DIHED =
>> 36.1946
>> VDWAALS = -9.6894 EEL = -19.9560 EGB =
>> -78.1446
>> 1-4 VDW = 14.2583 1-4 EEL = -46.5690 RESTRAINT =
>> 0.0000
>>
>>
>> NSTEP ENERGY RMS GMAX NAME NUMBER
>> 35000 -8.1184E+01 1.2796E-03 5.0121E-03 N9 50
>>
>> BOND = 2.1400 ANGLE = 20.5812 DIHED =
>> 36.1951
>> VDWAALS = -9.6875 EEL = -19.9644 EGB =
>> -78.1372
>> 1-4 VDW = 14.2586 1-4 EEL = -46.5699 RESTRAINT =
>> 0.0000
>>
>>
>> NSTEP ENERGY RMS GMAX NAME NUMBER
>> 36000 -8.1184E+01 1.2446E-03 3.6949E-03 C6 56
>>
>> BOND = 2.1398 ANGLE = 20.5802 DIHED =
>> 36.1955
>> VDWAALS = -9.6849 EEL = -19.9872 EGB =
>> -78.1156
>> 1-4 VDW = 14.2590 1-4 EEL = -46.5709 RESTRAINT =
>> 0.0000
>>
>> ... RESTARTED DUE TO LINMIN FAILURE ...
>>
>> ***** REPEATED LINMIN FAILURE *****
>>
>> ***** SEE http://ambermd.org/Questions/linmin.html FOR MORE INFO *****
>>
>>
>>
>>
>>
>>
>>
>> the strnage behavior is now, that some minimizations will finish without
>> this error and some will finish with this error.
>>
>>
>> Can anyone give me some help in solving this problem???
>> I appreciate your halp.
>>
>>
>> Best reegards
>>
>>
>> Jan Wahl
>> Goethe University/ Germany
>>
>> --
>> GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit
>> gratis Handy-Flat! http://portal.gmx.net/de/go/dsl
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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Received on Tue Jan 11 2011 - 07:30:06 PST
