On Tue, 2014-03-25 at 14:39 +0100, Urszula Uciechowska wrote:
> 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?
Your group input is still wrong. Repeating old advice: see the chapter
in the Amber manual regarding GROUP input.
As an alternative, use bellymask instead of the GROUP input.
I echo Dave's advice in using restraints rather than belly constraints,
for what it's worth.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Mar 25 2014 - 10:00:05 PDT
