Hi Bill and all Amber users,
I have figured out what is going on.
When aligning the original structure downloaded from the pdb, the input used for Glycam online (with optimized Asn, His, Gln), the Glycam output structure and the min.rst7 I noticed the following:
1. The original pdb from rcsb and the glycam input have the same coordinates
2. The glycam output does not align to either of these and shows differences in the HIR, HIT and GLR positions
3. The min.rst7 NE2 of HIR and HIT align to that of the glycam input while the rest of the ring aligns to the glycam output
Glycam does not recognize Zn so it is absent during the glycan addition. I chose to optimize the added glycans' positions with minimization using the online server.
The downloaded results gave the following sander_min.in file:
Constant Volume Minimization
# Control section
&cntrl
ntwe = 500, ntwx = 500, ntpr = 500,
nsnb = 25, dielc = 80, cut = 12.0,
ntb = 0,
maxcyc = 1000, ntmin = 1, ncyc = 1000, dx0 = 0.01, drms = 0.0001,
ntp = 0,
ibelly = 0, ntr = 0,
imin = 1,
ntr=1,
restraint_wt=100,
restraintmask=':',
/
It looks to me like all the residues were meant to be restrained while the glycans were perhaps minimized but because it specifies first ntr=0 and then ntr=1 maybe the protein atoms were minimized as well?
Is this an error in the sander_min.in used in the 'automatic' minimization on the Glycam server?
Since it was done in the absence of Zn it would make sense why the GLR, HIR, HIT positions now differ and trying to coordinate them to Zn then causes minimization failures.
I am thinking now of taking the glycam input pdb and just manually adding the glycan information and adjusting the N-linked asparagines' coordinates to the minimized ones. Does this seem like a reasonable thing to do?
Kind regards
Lizelle Lubbe
PhD (Medical biochemistry) candidate
Department of Integrative Biomedical Sciences
University of Cape Town
________________________________________
From: Lizelle Lubbe
Sent: 12 September 2017 02:05:32 PM
To: amber.ambermd.org; ross.cgl.ucsf.edu
Subject: Re: [AMBER] Minimization error due to modified residue
Hi Bill,
I've tried heating the system like you suggested but before that I repeated the minimization using a different approach. When ignoring the LINMIN failure and using the rst7 for heating it gives a SHAKE failure message. Seems like the minimization is not actually happening (thus the heating fails) because the NE2 .5686 of HIR (coordinating ZN) is stuck. When comparing the coordinates from different stages no differences are seen. I looked at the min1.rst7 in VMD and the NE2 is pulled towards ZN while the other atoms are obviously still fixed with the 50.0 restraint. The ring is then slightly distorted and not planar anymore (vs original pdb coordinates in green in attached picture) which might be causing the minimization failures. Is there any way to relieve this distortion? The coordinating HIT residue seems fine and planar - its atoms also do not show up in the min2-4.out.
>>> min1: all restrained but water and sodium
Constant Volume Minimization 1 with solute fixed
# Control section
&cntrl
imin=1,
irest = 0,
ntmin = 1, maxcyc = 2000, ncyc = 500, dx0 = 0.01, drms = 0.0001,
cut = 10.0,
ntb = 1,
ntp = 0,
ntr = 1, restraintmask='!:WAT= & !:Na+=', restraint_wt=50.0
/
This ran okay and gave a decrease in energy:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -4.9742E+05 1.8679E+02 7.8902E+04 HD11 1853
BOND = 1646.1825 ANGLE = 1451.4859 DIHED = 7285.2315
VDWAALS = 92386.2528 EEL = -651137.0367 HBOND = 0.0000
1-4 VDW = 3088.5186 1-4 EEL = 47864.3029 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
2000 -7.4216E+05 5.7349E-01 1.5388E+02 NE2 5686
BOND = 56487.2165 ANGLE = 1579.0072 DIHED = 6671.2399
VDWAALS = 134422.3740 EEL = -991996.4805 HBOND = 0.0000
1-4 VDW = 3047.4151 1-4 EEL = 47088.7467 RESTRAINT = 537.3320
EAMBER = -742700.4811
>>> min2: all restrained but water, sodium and H
Constant Volume Minimization 2 of solvent and H
# Control section
&cntrl
imin=1,
irest = 0,
ntmin = 1, maxcyc = 20000, ncyc = 10000, dx0 = 0.01, drms = 0.0001,
cut = 10.0,
ntb = 1,
ntc = 2,
ntf = 2,
ntp = 0,
ntr = 1, restraintmask='!:WAT,Na+ & !.H=', restraint_wt=50.0,
/
This terminated just after switch to conjugate gradient and no change in energy was found in any steps.
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -6.8624E+05 1.9239E+01 1.1716E+02 NE2 5686
BOND = 570.5312 ANGLE = 1577.7678 DIHED = 6671.1227
VDWAALS = 134688.1498 EEL = -879896.8929 HBOND = 0.0000
1-4 VDW = 3049.4880 1-4 EEL = 47099.9488 RESTRAINT = 0.0276
EAMBER = -686239.8846
NSTEP ENERGY RMS GMAX NAME NUMBER
10100 -6.8624E+05 1.9238E+01 1.1264E+02 NE2 5686
BOND = 570.1572 ANGLE = 1577.8493 DIHED = 6671.0580
VDWAALS = 134675.5837 EEL = -879880.8124 HBOND = 0.0000
1-4 VDW = 3049.4902 1-4 EEL = 47099.6597 RESTRAINT = 0.0260
EAMBER = -686237.0143
... RESTARTED DUE TO LINMIN FAILURE ...
***** REPEATED LINMIN FAILURE *****
>>> min3: all free except backbone atoms
Constant Volume Minimization 3 with backbone fixed
# Control section
&cntrl
imin=1,
irest = 0,
ntmin = 1, maxcyc = 20000, ncyc = 10000, dx0 = 0.01, drms = 0.0001,
cut = 10.0,
ntb = 1,
ntp = 0,
ntc = 2, ntf = 2,
ntr = 1, restraintmask=':1-612 & .CA,C,O,N', restraint_wt=10.0
/
Ignored error in min2 and used min2.rst7 for min3 input.
Again no change in energy and Linmin failure after switch to conjugate gradient
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -6.8624E+05 1.9238E+01 1.1268E+02 NE2 5686
BOND = 570.1572 ANGLE = 1577.8493 DIHED = 6671.0580
VDWAALS = 134675.5812 EEL = -879880.8074 HBOND = 0.0000
1-4 VDW = 3049.4902 1-4 EEL = 47099.6596 RESTRAINT = 0.0000
EAMBER = -686237.0119
NSTEP ENERGY RMS GMAX NAME NUMBER
10100 -6.8623E+05 1.9237E+01 1.0836E+02 NE2 5686
BOND = 569.7907 ANGLE = 1577.9320 DIHED = 6671.0013
VDWAALS = 134663.0421 EEL = -879864.6675 HBOND = 0.0000
1-4 VDW = 3049.4929 1-4 EEL = 47099.3767 RESTRAINT = 0.0000
EAMBER = -686234.0317
... RESTARTED DUE TO LINMIN FAILURE ...
***** REPEATED LINMIN FAILURE *****
>>>min4: whole system free
Constant Volume Minimization 4 without restraints
# Control section
&cntrl
imin=1,
irest = 0,
ntmin = 1, maxcyc = 20000, ncyc = 10000, dx0 = 0.01, drms = 0.0001,
cut = 10.0,
ntb = 1,
ntp = 0,
ntc = 2, ntf = 2,
ntr = 0,
/
Ignored error in min3 and used min3.rst7 for min4 input.
Again no change in energy and Linmin failure after switch to conjugate gradient
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -6.8623E+05 1.9237E+01 1.0836E+02 NE2 5686
BOND = 569.7906 ANGLE = 1577.9320 DIHED = 6671.0013
VDWAALS = 134663.0356 EEL = -879864.6576 HBOND = 0.0000
1-4 VDW = 3049.4929 1-4 EEL = 47099.3766 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
10100 -6.8623E+05 1.9237E+01 1.0416E+02 NE2 5686
BOND = 569.4274 ANGLE = 1578.0164 DIHED = 6670.9519
VDWAALS = 134650.4545 EEL = -879848.5176 HBOND = 0.0000
1-4 VDW = 3049.4961 1-4 EEL = 47099.0930 RESTRAINT = 0.0000
... RESTARTED DUE TO LINMIN FAILURE ...
***** REPEATED LINMIN FAILURE *****
>>>Tried to use min4.rst7 as input for heating
Heating
# Control section
&cntrl
imin = 0,
irest = 0,
ntx = 1,
nstlim = 300000, dt = 0.002,
ntc = 2, ntf = 2,
tempi = 10.0, temp0 = 300.0,
ntwx = 5000, ntpr = 5000, ntwe = 5000,
ntb = 1, ntp = 0,
ntt = 3, gamma_ln = 2, ig=-1,
cut = 10.0,
ntr = 0,
ntxo = 2,
ioutfm = 1,
iwrap = 1,
/
&wt type='TEMP0', istep1=0, istep2=100000, value1=10.0, value2=100.0/
&wt type='TEMP0', istep1=100001, istep2=200000, value1=100.0, value2=200.0/
&wt type='TEMP0', istep1=200001, istep2=300000, value1=200.0, value2=300.0/
&wt type='END'/
This gave a SHAKE error due to atoms 12494-5 (WAR .O and .H1)
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 2 6058 12494 12495
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
--------------------------------------------------------------------------
Kind regards
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 04:57 PM
To: amber.ambermd.org
Subject: Re: [AMBER] Minimization error due to modified residue
I would read up on equilibration, maybe start at 10K and go to 100K in a
100,000 steps (more for a bigger system), and assess.
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 Tue Sep 12 2017 - 08:00:05 PDT
