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 - 20:30:02 PDT
