One good thing is that, unlike before at step 5000, this time I don't have distortion of the metal site (no overlap of atoms). Nothing jumps out as being very strange when viewing the coordinates of the first 5000 steps.
Lizelle
________________________________________
From: Lizelle Lubbe <LBBLIZ002.myuct.ac.za>
Sent: 11 September 2017 04:03:57 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Minimization error due to modified residue
Okay I just tried that. When trying to minimize the solvent while having ntc=ntf=2 it failed due to LINMIN error
___________________________________________________________________________________________________________________
min1.out:
... RESTARTED DUE TO LINMIN FAILURE ...
NSTEP ENERGY RMS GMAX NAME NUMBER
600 -5.5571E+05 1.4422E+01 1.0911E+02 Zn 12493
BOND = 524.4219 ANGLE = 1593.8799 DIHED = 6681.1564
VDWAALS = 36245.1401 EEL = -651519.6869 HBOND = 0.0000
1-4 VDW = 3068.4211 1-4 EEL = 47143.0466 RESTRAINT = 557.1118
EAMBER = -556263.6209
... RESTARTED DUE TO LINMIN FAILURE ...
***** REPEATED LINMIN FAILURE *****
***** SEE
http://ambermd.org/Questions/linmin.html FOR MORE INFO *****
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
614 -5.5571E+05 1.4422E+01 1.0911E+02 Zn 12493
BOND = 524.4219 ANGLE = 1593.8799 DIHED = 6681.1564
VDWAALS = 36245.1392 EEL = -651519.6849 HBOND = 0.0000
1-4 VDW = 3068.4211 1-4 EEL = 47143.0466 RESTRAINT = 557.1117
EAMBER = -556263.6199
_______________________________________________________________________________________________________________________________
This link mentioned that having SHAKE on can cause this error and that initial minimization should be done without it.
When using min1.rst7 from successful minimization1 without SHAKE then minimization 2 with ntc=ntf=2 also failed due to LINMIN error. Atom 5686 is the NE2 of HIR that coordinates the ZN
Any other ideas as to what I can do to solve this problem?
min2.out:
NSTEP ENERGY RMS GMAX NAME NUMBER
5000 -6.8624E+05 1.9238E+01 1.1379E+02 NE2 5686
BOND = 570.2513 ANGLE = 1577.8284 DIHED = 6671.0734
VDWAALS = 134678.7301 EEL = -879884.8564 HBOND = 0.0000
1-4 VDW = 3049.4894 1-4 EEL = 47099.7304 RESTRAINT = 0.0000
... RESTARTED DUE TO LINMIN FAILURE ...
... RESTARTED DUE TO LINMIN FAILURE ...
NSTEP ENERGY RMS GMAX NAME NUMBER
5050 -6.8624E+05 1.9238E+01 1.1379E+02 NE2 5686
BOND = 570.2511 ANGLE = 1577.8284 DIHED = 6671.0733
VDWAALS = 134678.7224 EEL = -879884.8458 HBOND = 0.0000
1-4 VDW = 3049.4894 1-4 EEL = 47099.7303 RESTRAINT = 0.0000
... RESTARTED DUE TO LINMIN FAILURE ...
... RESTARTED DUE TO LINMIN FAILURE ...
NSTEP ENERGY RMS GMAX NAME NUMBER
5100 -6.8624E+05 1.9238E+01 1.1378E+02 NE2 5686
BOND = 570.2508 ANGLE = 1577.8285 DIHED = 6671.0733
VDWAALS = 134678.7124 EEL = -879884.8334 HBOND = 0.0000
1-4 VDW = 3049.4894 1-4 EEL = 47099.7300 RESTRAINT = 0.0000
... RESTARTED DUE TO LINMIN FAILURE ...
***** REPEATED LINMIN FAILURE *****
***** SEE
http://ambermd.org/Questions/linmin.html FOR MORE INFO *****
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
5114 -6.8624E+05 1.9238E+01 1.1378E+02 NE2 5686
BOND = 570.2507 ANGLE = 1577.8285 DIHED = 6671.0733
VDWAALS = 134678.7100 EEL = -879884.8302 HBOND = 0.0000
1-4 VDW = 3049.4894 1-4 EEL = 47099.7299 RESTRAINT = 0.0000
Lizelle Lubbe
PhD (Medical biochemistry) candidate
Department of Integrative Biomedical Sciences
University of Cape Town
________________________________________
From: Lizelle Lubbe <LBBLIZ002.myuct.ac.za>
Sent: 11 September 2017 03:12 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Minimization error due to modified residue
No I did not. Thought that it should be off for the minimization and then on for equilibration.
Will try minimization1 now with ntc=2 and ntf=2
Thanks Bill
Kind regards
Lizelle
________________________________________
From: Bill Ross <ross.cgl.ucsf.edu>
Sent: 11 September 2017 03:09:40 PM
To: amber.ambermd.org
Subject: Re: [AMBER] Minimization error due to modified residue
Are you using ntc=2, ntf=2?
This would be required to keep TIP3 H's within the boundary of the O vdw
radius, since the H's have no radius.
Bill
On 9/11/17 5:38 AM, Lizelle Lubbe wrote:
> the atoms 6143 OE1 of GLR389 (the ZN-coordinated Glu) and 12495 H1 of WAR (the ZN-coordinated TIP3p water) overlap
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Received on Mon Sep 11 2017 - 07:30:03 PDT
