I'm not sure which H you're referring to... Previously the H from WAR was attracted to the OE1 of GLR
________________________________________
From: Bill Ross <ross.cgl.ucsf.edu>
Sent: 11 September 2017 04:28:24 PM
To: amber.ambermd.org
Subject: Re: [AMBER] Minimization error due to modified residue
One thing I didn't think of is, why would an H be attracted to a Zn
anyway, assuming both have positive charge.
Bill
On 9/11/17 7:03 AM, Lizelle Lubbe wrote:
> 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 - 08:00:03 PDT
