Dear Lizelle,
Are you using Amber on a GPU code?
Regards,
Shafaq
________________________________
From: Lizelle Lubbe <LBBLIZ002.myuct.ac.za>
Sent: Monday, September 11, 2017 3:48:26 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Minimization error due to modified residue
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 - 08:00:06 PDT
