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:
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Amber 6 SANDER Scripps/UCSF 1999
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| 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
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Received on Wed Sep 13 2000 - 11:48:24 PDT
