HI
your GMAX and energy terms are too high. You might want to visualise
the coordinate file before minimisation and after, and look at atom names
C24.
There is perhaps an overlap of atoms.
Best Regards
Elvis
On Fri, 25 Sep 2020 at 08:39, Xinye Wang <xywung.163.com> wrote:
> Dear Amber community,
> I am running minimization for protein-ligand system, its showing the
> following error after step 2000
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
>
> 2000 1.6209E+06 3.1751E+02 3.7073E+04 C24 5380
>
>
>
>
> BOND = 892134.9355 ANGLE = 6431.5058 DIHED =
> 4461.1631
>
> VDWAALS = 480066.2046 EEL = -170572.5894 HBOND =
> 0.0000
>
> 1-4 VDW = 394876.4985 1-4 EEL = 12361.8778 RESTRAINT =
> 1173.5231
>
> EAMBER = 1619759.5959
>
>
>
>
> .... RESTARTED DUE TO LINMIN FAILURE ...
>
>
>
>
> .... RESTARTED DUE TO LINMIN FAILURE ...
>
>
>
>
> What parameters should I change in the input file? The parameters that I
> used are listed as below:
>
> Minimize1
>
> &cntrl
>
> imin=1,
>
> maxcyc=4000,
>
> ncyc=2000,
>
> ntb=1,cut=12.0,ntr=1,ntxo=1,
>
> restraint_wt=3000.0,
>
> restraintmask=':1-345’,
>
> /
>
> Minimize2
>
> &cntrl
>
> imin=1,
>
> maxcyc=4000,
>
> ncyc=2000,
>
> ntb=1,cut=12.0,ntr=1,ntxo=1,
>
> restraint_wt=500.0,
>
> restraintmask=':1-341.CA,N,C|:342-344|:345&!.H=',
>
> /
>
> Minimize3
>
> &cntrl
>
> imin=1,
>
> maxcyc=4000,
>
> ncyc=2000,
>
> ntb=1,cut=12.0,ntxo=1,
>
> /
>
>
>
> Thank you in advance
>
>
> Xinye Wang
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>
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Received on Thu Sep 24 2020 - 20:30:02 PDT
