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I doing some simple min and md on a zink-protein using
amber. I want to keep an zink-binding-side fixed and
put small restraints on CA-atoms. I use the same group
specification at the end of both min- and
md-inputfiles. While the min is not a problem, the md
run using the coordinates from the minimization stops
after 3-27 steps with the error message:
COORDINATE RESETTING CANNOT BE ACCOMPLISHED,DEVIATION
IS TOO LARGE
NITER, NIT, LL, I AND J ARE : 0 1 4235 8503 8504
What does this mean ? Everything else in the
outputfile is OK (restraints read, group input read,
etc) !
Here my md-inputfile
&cntrl
irest=0, ibelly=0, imin=0,
nrun=10, ntt=5,
nstlim=1000,
ntc=3,
ntf=3, idiel=1,
cut=9.0, scnb=2.0, scee=1.2,
ntpr=200, ntwx=200, ntwe=200,
ntr=1, nmrmax=1,
&end
&wt TYPE='TEMP0', ISTEP1=0, ISTEP2=1000,
VALUE1=0.0, VALUE2=300.0, &end
&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, &end
&wt TYPE='TEMP0', ISTEP1=3001, ISTEP2=8000,
VALUE1=600.0, VALUE2=600.0, &end
&wt TYPE='TEMP0', ISTEP1=8001, ISTEP2=10000,
VALUE1=600.0, VALUE2=000.0, &end
&wt TYPE='END', &end
LISTOUT=POUT
LISTIN=POUT
# NMR-restraints: 693 ZINC ZN 526 HIE NE2 2.027
&rst iat=11117,8503, r3= 2.03, r4= 2.53,
r1 = 1.3, r2 = 1.8, rk2=0.0, rk3=100.0, ir6=1,
&end
# NMR-restraints: 693 ZINC ZN 530 HIE NE2 2.014
&rst iat=11117,8568, r3= 2.02, r4= 2.52, &end
# NMR-restraints: 693 ZINC ZN 589 GLU OE1 1.955
&rst iat=11117,9477, r3= 1.94, r4= 2.44, &end
&rst iat=0, &end
group input: restraints on Ca-atoms
25
FIND
CA * * *
SEARCH
RES 1 693
END
group input: restraints on Zn 693
9999
RES 693
END
group input: restraints on Res 526
9999
RES 526
END
group input: restraints on Res 530
9999
RES 530
END
group input: restraints on Res 589
9999
RES 589
END
END
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Received on Mon Aug 27 2001 - 01:46:51 PDT
