dear Gusztav
the problem is probably that the box size was not handled as it should be
by sander.
If its a restart the box size is at the bottom of the input coord file,
else its at the bottom of parm file. The code should have figured all this
out better, but hopefully that will improve with next release. Meanwhile,
get the box sizes from one of the two above two files and input it in the
ewald section as follows:
&ewald
a = ..., b = ..., c = ..., alpha = 90.0, beta = 90.0, gamma = 90.0,
&end
where the ... are the three box sizes for first second and third box
dimensions. alpha,beta,gamma are unit cell angles (here all 90 deg.).
hope this helps
Tom D
On Wed, 13 Sep 2000 schayg_at_puskin-a206.sote.hu wrote:
> Dear amber users,
> I have tried to run short dynamics on the BPTI example protein, and sander
> refuses to do so, it is complaining about some Ewald parameters to be out
> of range.
> I have recompiled AMBER with MAXBONDS=8, the original setup did not have
> this problem.
> I also checked ew_legal.h and set the upper limit to 1.0d2
>
> does anyone know what could be the problem?
> Thank you,
> Gusztav Schay.
>
>
> here is sander's output:
>
> -------------------------------------------------------
> Amber 6 SANDER Scripps/UCSF 1999
> -------------------------------------------------------
>
> | Mon Sep 11 15:31:24 2000
>
>
> File Assignments:
> |MDIN : mdrun.in
> |MDOUT: mdrun.out
> |INPCR: prmcrd
> |PARM : prmtop
> |RESTR: mdrun.out.rst
> |REFC : refc
> |MDVEL: mdvel
> |MDEN : mden
> |MDCRD: mdcrd
> |MDINF: mdinfo
>
>
> Here is the input file:
>
> molecular dynamics run (short)
> &cntrl
> imin=0, irest=0, ntx=1, tempi=0.,
> ntt=1, temp0=300.0, tautp=0.2,
> ntp=2, taup=0.2,
> ntb=2, ntc=2, ntf=2,
> nstlim=500,
> ntwe=100, ntwx=100, ntpr=25,
> &end
> -------------------------------------------------------------------------------
>
> molecular dynamics run (short)
>
>
>
> 1. RESOURCE USE:
>
> getting box info from bottom of parm
> getting new box info from bottom of inpcrd
> | peek_ewald_inpcrd: Box info not found in inpcrd
>
> EWALD SPECIFIC INPUT:
>
> -------------------------------------------------
> NO EWALD INPUT FOUND: USING DEFAULTS
> -------------------------------------------------
> Largest sphere to fit in unit cell has radius = nan
>
> Ewald PARAMETER RANGE CHECKING:
> parameter skinnb+cutoffnb: (nonbond list cut) has value 0.90000E+01
> This is outside the legal range
> Lower limit: 0.00000E+00 Upper limit: NAN
> Check ew_legal.h
>
> -------------
>
>
>
>
>
> -----------------------
> Gusztav SCHAY
> PhD student
> Semmelweis University Budapest
> Dept. of Biophysics and Radiation Biology
> Budapest
> Puskin u. 9.
> H-1088
> Hungary
>
> phone: +36-1-2662755 #4033
> email: schayg_at_puskin-a206.sote.hu
> -----------------------
>
>
>
Received on Wed Sep 13 2000 - 15:29:16 PDT
