Hi,
Thank you for you reply. However after changing the input as you suggested
in the out file I am getting:
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme =
1
vdwmeth = 1, eedmeth = 1, netfrc = 0
Box X = 104.479 Box Y = 104.479 Box Z = 104.479
Alpha = 109.471 Beta = 109.471 Gamma = 109.471
NFFT1 = 108 NFFT2 = 108 NFFT3 = 108
Cutoff= 12.000 Tol =0.100E-04
Ewald Coefficient = 0.22664
Interpolation order = 4
Warning: Although EWALD will work with belly
(for equilibration), it is not strictly correct!
LOADING THE BELLY ATOMS AS GROUPS
----- READING GROUP 1; TITLE:
Belly on water molecules
rfree: Error decoding variable 2 2 from:
RES WAT
this indicates that your input contains
incorrect information
field 2 was supposed to
have a (1=character, 2=integer, 3=decimal) value
How can I fix this problem?
Thank you for your help.
Urszula
> Hi,
>
> The line after the '/' is a title line. So sander thinks that "RES WAT"
> is a title. Add a blank line and it should be fine. Like:
>
> &cntrl
> imin = 1,
> maxcyc = 2000,
> ncyc = 500,
> cut = 12,
> ntb = 1,
> ibelly = 1,
> /
> Belly on water molecules
> RES WAT
> END
> END
>
> Sincerely,
>
> Gerald.
>
> On 03/25/2014 01:13 PM, Urszula Uciechowska wrote:
>> Dear Amber users,
>>
>> My complex contains DNA and protein. I would like to use ibelly to keep
>> frozen the complex and allowed water to move. My input file contains:
>>
>> energy minimization for DNA and protein
>> &cntrl
>> imin = 1,
>> maxcyc = 2000,
>> ncyc = 500,
>> cut = 12,
>> ntb = 1,
>> ibelly = 1,
>> /
>> RES WAT
>> END
>> END
>>
>> after short run, calculations stopped:
>> the out file contains>
>>
>> Warning: Although EWALD will work with belly
>> (for equilibration), it is not strictly correct!
>>
>>
>> LOADING THE BELLY ATOMS AS GROUPS
>>
>> ----- READING GROUP 1; TITLE:
>> RES WAT
>> Number of atoms in this group = 0
>> ----- END OF GROUP READ -----
>>
>> --------------------------------------------------------------------------------
>> 3. ATOMIC COORDINATES AND VELOCITIES
>> --------------------------------------------------------------------------------
>>
>>
>> begin time read from input coords = 0.000 ps
>>
>> Number of triangulated 3-point waters found: 0
>>
>> Sum of charges from parm topology file = 0.00000017
>> Forcing neutrality...
>>
>> --------------------------------------------------------------------------------
>> 4. RESULTS
>> --------------------------------------------------------------------------------
>>
>> ---------------------------------------------------
>> APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
>> using 5000.0 points per unit in tabled values
>> TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
>> | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
>> | CHECK d/dx switch(x): max rel err = 0.7967E-11 at 2.716640
>> ---------------------------------------------------
>> | Local SIZE OF NONBOND LIST = 0
>> | TOTAL SIZE OF NONBOND LIST = 0
>>
>>
>> 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
>>
>> what is wrong?
>>
>> best regards
>> Urszula
>>
>>
>> -----------------------------------------
>> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
>> http://www.ug.edu.pl/
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
> --
> ____________________________________________________________________________
>
> Prof. Gerald MONARD
> SRSMC, Université de Lorraine, CNRS
> Boulevard des Aiguillettes B.P. 70239
> F-54506 Vandoeuvre-les-Nancy, FRANCE
>
> e-mail : Gerald.Monard.univ-lorraine.fr
> tel. : +33 (0)383.684.381
> fax : +33 (0)383.684.371
> web : http://www.monard.info
>
> ____________________________________________________________________________
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
-----------------------------------------
Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
http://www.ug.edu.pl/
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Received on Tue Mar 25 2014 - 07:00:02 PDT
