Hi
I am not sure if the carbocation has anything to do with this.
However,
NSTEP ENERGY RMS GMAX NAME NUMBER
2000 1.6209E+06 3.1751E+02 3.7073E+04 C24 5380
This indicates that atom numbered 5380 which is C24 has the
largest gradient which you must visualise and find out why.
VDWAALS = 480066.2046 is also a very large positive value indicative of
some overlap in the system.
Also, I see that you apply a very large restraining force (3000
kcal/mol/A), and therefore, your system is practically fixed.
Best Regards
Elvis
On Fri, 25 Sep 2020 at 09:09, Xinye Wang <xywung.163.com> wrote:
> Thank you, Elvis.
>
>
> There is a carbocation in the ligand, but not C24. Does it have important
> effect on the minimization step?
>
>
> Best,
>
>
> Xinye
> On 09/25/2020 11:20，Elvis Martis<elvis_bcp.elvismartis.in> wrote：
> 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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Received on Thu Sep 24 2020 - 21:30:03 PDT
