AMBER Archive (2001)

Subject: beginners problem (fwd)

From: jim caldwell (caldwell_at_heimdal.compchem.ucsf.edu)
Date: Mon Jul 30 2001 - 10:16:28 CDT

---------- Forwarded message ----------
Date: Mon, 30 Jul 2001 15:19:04 +0200 (CEST)
From: Guido Hansen <guidohansen_at_yahoo.de>
To: amber_at_heimdal.compchem.ucsf.edu
Subject: beginners problem

I doing some simple md on a zink-protein using amber
for the first time. So maybe some of you amber cracks
out there can help me:
Shortly after starting the md run I get the message:
"segmentation fault(core dumped)". I am using a SGI
indigo workstation. Here my md input file:

   # Dynamics - constrains on CA and Zn
 &cntrl
   IMIN=0, IBELLY=1,
   MAXCYC=1000,
   NTT=5, NTC=3, NTF=3,
   NRUN=10, nstlim=1000,
   IDIEL=1, DRMS=0.005,
   ntwe=200, ntwx=200, ntpr=200,
   CUT=9.00, SCEE=1.2,
   NTPR=100, NTR= 0
 &end
 &wt TYPE='TEMP0', ISTEP1=0, ISTEP2=1000,
     VALUE1=0.0, VALUE2=300.0
 &wt TYPE='TEMP0', ISTEP1=1001, ISTEP2=2000,
     VALUE1=300.0, VALUE2=300.0, &end
 &wt TYPE='TEMP0', ISTEP1=2001, ISTEP2=3000,
     VALUE1=300.0, VALUE2=600.0
 &wt TYPE='TEMP0', ISTEP1=3001, ISTEP2=8000,
     VALUE1=600.0, VALUE2=600.0
 &wt TYPE='TEMP0', ISTEP1=8001, ISTEP2=10000,
     VALUE1=600.0, VALUE2=000.0
 &wt TYPE='END', &end
# ibelly-run: sidechains free
FIND
* * S *
* * B *
* * 3 *
* * E *
SEARCH
RES 1 693
END
# ibelly-run: loop 2 free
RES 257 261
END
# ibelly-run: loop 3 free
RES 495 496
END
# ibelly-run: water free
RES 694 1857
END

thanks in advance,
Guido Hansen

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