You would need to visualize your structures, trying to find atoms 805
and 805, which are the offending culprits.
Adrian
On 7/15/21 4:32 PM, Rana Rehan Khalid wrote:
> [External Email]
>
> Dear Amber users
>
> I generated the mutant models (a dimer structure), Most of these mutant
> models md runs are fine but some models failed during heating, I checked
> the earlier threads
> following things I have applied
>
> 1. I ran the annealing through pmemd.cuda and then also try it with sander
> 2. I also follow this thread https://urldefense.proofpoint.com/v2/url?u=http-3A__archive.ambermd.org_201004_0189.html&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=mqbeZu_9ow7-VOecNfhZsPkVczdNDPVxAqiLY7jbGiI&s=7T8oTqQDL8N2PkRMve1zlaV63Ix1_f6wY_qQ8N78jqU&e=
> 3. I also used H++ to make my initial structure good. I also used the pqr
> file of this complex. I thought maybe the initial structure was not good.
>
> but facing the same error. My error is
>
> vlimit exceeded for step 1; vmax = 74.4479
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 0 1059 805 804
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>
> I used this input file for heating
>
>
> Heat
> &cntrl
> imin=0,
> ntx=1,
> irest=0,
> nstlim=50000,
> dt=0.002,
> ntf=2,
> ntc=2,
> tempi=0.0,
> temp0=300.0,
> ntpr=1000,
> ntwx=1000,
> cut=10.0,
> ntb=1,
> ntp=0,
> ntt=3,
> gamma_ln=2.0,
> nmropt=1,
> ig=-1,
> /
> &wt type='TEMP0', istep1=0, istep2=9000, value1=0.0, value2=300.0 /
> &wt type='TEMP0', istep1=9001, istep2=10000, value1=300.0, value2=300.0 /
> &wt type='END' /
>
> Kindly guide me how I can resolve this issue.
>
> Thank you for your time in advance.
>
> Best
> Rehan
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--
Dr. Adrian E. Roitberg
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Thu Jul 15 2021 - 14:00:03 PDT
