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
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Received on Tue Mar 25 2014 - 06:30:03 PDT
