Hi,
you need to look at the test cases and follow that a bit. We are working
on some tutorials, but they are not yet ready.
I would look at your dist_vs_t file, specially the first line.
If your distance at time zero is really 29 A and you start from 29.5,
the initial restraint will be huge. Given that your initial restraint
energy is 3334.5521 and your force constant is 5000, you seems to have a
distance of ~0.8 A away from where you should be.
this causes a very fastm strong pull, followed by shake failures.
Try stating your pull at exactly the distance you really have before
pulling.
Adrian
On 3/23/10 5:41 AM, nicholus bhattacharjee wrote:
> Dear community,
> I am trying to do a steered MD of a protein of 56
> residue long. The initial distance between CA atom of 1st residue (atom no
> 2) and CA atom of 56th residue (atom no 905) is 29A. My input and dist.RST
> files are as follows
>
>
> pro.in>
>
> Sample pulling input
> &cntrl
> nstlim=5000000, cut=99.0, igb=1, saltcon=0.1,
> ntpr=500, ntwr=500, ntt=1,
> ntx=1, ntwx=500, ig=256251,
> ntc=2, ntf=2, tol=0.000001,
> dt=0.002, ntb=0, tempi=300., temp0=300.,
> jar=1
> /
> &wt type='DUMPFREQ', istep1=1, /
> &wt type='END', /
> DISANG=dist.RST
> DUMPAVE=dist_vs_t
> LISTIN=POUT
> LIST=POUT
>
> dist.RST>
>
> # Change
> &rst iat=905,2, r2=29.5, rk2=5000., r2a=50.0, /
>
>
> The output is file is giving errors
>
>
> 4. RESULTS
> --------------------------------------------------------------------------------
>
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 343.74 PRESS =
> 0.0
> Etot = 3687.1261 EKtot = 778.3610 EPtot =
> 2908.7651
> BOND = 12.4186 ANGLE = 207.4832 DIHED =
> 678.5772
> 1-4 NB = 802.1944 1-4 EEL = 3296.4852 VDWAALS =
> 14.2383
> EELEC = -3938.2112 EGB = -1498.9728 RESTRAINT =
> 3334.5521
> EAMBER (non-restraint) = -425.7870
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 3334.552 Angle = 0.000 Torsion = 0.000
> ===============================================================================
> vlimit exceeded for step 0; vmax = 302.9507
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 1 7 1 2
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>
> I dont know what to do. Please help. By the way is there any tutorial for
> steered MD for Amber 9.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project
Department of Chemistry
Senior Editor. Journal of Physical Chemistry
American Chemical Society
University of Florida PHONE 352 392-6972
P.O. Box 118435 FAX 352 392-8722
Gainesville, FL 32611-8435 Email adrian.qtp.ufl.edu
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Received on Tue Mar 23 2010 - 07:30:04 PDT
