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 - 21:00:03 PDT
