Hi!
Recently i had the same problem.i tackled by changing the box size.
Have u given REFRENCE cordinate file when u are putting constraints? And
also u ckeck the box size.This problem is also discussed on the AMBER
Website
madhu
On Mon, 27 Aug 2001, [iso-8859-1] Guido Hansen wrote:
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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 - 05:50:59 PDT
