> So are you saying that as long as the min2 structure looks fine
although it gives a LINMIN error you can proceed to heating and
equilibration?
If any police stop you, tell them I said it was ok. If you wreck your
computer, it's all on you, though. :-)
If it warms up ok, I will never tell anyone this happened. If not, more
debugging!
Bill
On 9/11/17 7:48 AM, Lizelle Lubbe wrote:
> So are you saying that as long as the min2 structure looks fine although it gives a LINMIN error you can proceed to heating and equilibration?
>
> Would you consider this heating input to be slow enough?
>
> Heating
>
> # Control section
> &cntrl
> imin = 0,
> irest = 0,
> ntx = 1,
> ntb = 1, ntp = 0,
> cut = 10.0,
> ntc = 2, ntf = 2,
> tempi = 0.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 2, ig=-1,
> nstlim = 50000, dt = 0.002,
> ntwx = 5000, ntpr = 5000, ntwe = 5000,
> ioutfm = 1,
> iwrap = 1,
> ntr = 1, restraintmask=':1-721,756', restraint_wt=10.0,
> /
>
>
> Lizelle Lubbe
>
> PhD (Medical biochemistry) candidate
> Department of Integrative Biomedical Sciences
> University of Cape Town
> ________________________________________
> From: Bill Ross <ross.cgl.ucsf.edu>
> Sent: 11 September 2017 04:37:24 PM
> To: amber.ambermd.org
> Subject: Re: [AMBER] Minimization error due to modified residue
>
> My mistake. I suspect the LINMIN failure you are seeing now is because
> of the charge of the Zn, and may be 'just life'. I would try to warm up
> slowly, and watch the Zn area with VMD.
>
> Bill
>
>
> On 9/11/17 7:30 AM, Lizelle Lubbe wrote:
>> 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 - 08:00:05 PDT
