AMBER Archive (2003)

Subject: run sander?

From: quch quch (quch0_at_yahoo.com)
Date: Mon Jun 02 2003 - 11:22:35 CDT

Hi,
I have problem to run sander on test file, could
anyone tell me what is wrong with the input file?

Input file ($AMBERHOME/test/vac_rna):
===========================================
 test of vacuum minimization, on a stretch of A-RNA
 &cntrl
                        
   cut=99.0, igb=0, imin=1,
   ntpr=1, ntwr=100000, ntt=0,
   ntb=0,
   maxcyc=10,
 &end
 &ewald
   eedmeth=5,
 &end
======================================
after sander:

mpirun -np 1 sander -O -i gbin -c md4.x -o test.out

Output has errors like this:
=============================
   1. RESOURCE USE:

   EWALD SPECIFIC INPUT:

| Using the SGI specific (ZFFT3D) Fast Fourier
Transform
| Using the T3D specific (FFT3D0) Fast Fourier
Transform
     Largest sphere to fit in unit cell has radius =
  0.000

 Ewald PARAMETER RANGE CHECKING:
 parameter skinnb+cutoffnb: (nonbond list cut) has
value 0.10000E+03
 This is outside the legal range
 Lower limit: 0.00000E+00 Upper limit: 0.00000E+00
 Check ew_legal.h
============================

Thanks,

qu

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