hi,
I changed it to RES but still getting error:
My input file is the following:
energy minimization
&cntrl
imin = 1,
maxcyc = 2000,
ncyc = 250,
cut = 10,
ntb = 1,
ntr = 1,
/
Hold the DNA-protein fixed
RES 1 289
END
END
in out I have:
5. REFERENCE ATOM COORDINATES
----- READING GROUP 1; TITLE:
Hold the DNA-protein fixed
rfree: Error decoding variable 1 3 from:
RES
this indicates that your input contains
incorrect information
field 1 was supposed to
have a (1=character, 2=integer, 3=decimal) value
I am using now AMBER11 and have no how to correct it.
/Urszula
> On Tue, Mar 25, 2014, Urszula Uciechowska wrote:
>>
>> My complex contains DNA and protein. I would like to use ibelly to keep
>> frozen the complex and allowed water to move.
>
> I'd advise against that (but then I always do!) Consider using restraints
> to
> the initial position (ntr=1) rather than the belly.
>
>>
>> energy minimization for DNA and protein
>> &cntrl
>> imin = 1,
>> maxcyc = 2000,
>> ncyc = 500,
>> cut = 12,
>> ntb = 1,
>> ibelly = 1,
>> /
>> RES WAT
>> END
>> END
>>
>> LOADING THE BELLY ATOMS AS GROUPS
>>
>> ----- READING GROUP 1; TITLE:
>> RES WAT
>> Number of atoms in this group = 0
>
> Note that your group syntax is wrong, and is selecting zero atoms. See
> the
> chapter on group selections in the Manual.
>
>> NSTEP ENERGY RMS GMAX NAME
>> NUMBER
>> 1 -1.0972E+06 NaN 0.0000E+00 N 1
>>
>> BOND = 0.0000 ANGLE = 0.0000 DIHED =
>> 0.0000
>> VDWAALS = -624.5497 EEL = -1096564.5563 HBOND =
>> 0.0000
>> 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
>> 0.0000
>
> It's not clear what caused RMS to be NaN (not a number). You should
> experiment with the input parameters (running short, say 10-step
> simulations
> with ntpr=1) until you can get something to work. The fact that you have
> no
> bond, angle, etc. energies is suspicious: I suspect that the code may well
> have a bug if you set ibelly=1, but choose no atoms to be in the belly.
>
> Don't be afraid to experiment and try to see what will work.
>
> ....dac
>
>
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>
>
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Received on Tue Mar 25 2014 - 07:30:02 PDT
