[gmx-users] energy minimisation - LINCS WARNING

[Nash, Anthony]

Hi Justin,


I’ve tried out all of your suggestions, they worked to an extent but the
in vacu idea was a good call as it’s actually helped me isolate what the
real problem is: I-TASSER has put the C-N backbone bond of two residues
through the ring of an adjacent PHE residue!

Thanks
Anthony 


On 02/10/2016 23:16, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on
behalf of Justin Lemkul"
<gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
jalemkul at vt.edu> wrote:

>
>Please don't reply to digests or unrelated threads when starting a new
>topic; it 
>creates a mess in the archive.
>
>On 10/2/16 6:11 PM, Nash, Anthony wrote:
>> Hi all,
>>
>> I had a homology/de-novo model .pdb converted into .gro, solvated,
>> neutralised and now I¹m going through a series of energy minimisation
>> steps. Unfortunately, during energy minimisation I get LINCS WARNINGS
>> (angle relative constraint deviation). The the naked eye, the atoms
>> involved don¹t look untoward.
>>
>>
>> When I used LINCS all-bond I get the following error:
>> -----------------------------------
>>
>> Step -1, time -0.001 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.001657, max 0.033500 (between atoms 1362 and 1363)
>> bonds that rotated more than 30 degrees:
>>  atom 1 atom 2  angle  previous, current, constraint length
>>
>>
>>
>> When I reduced this to only be the hydrogen bonds (h-bonds) I get:
>> -----------------------------------
>> Step 20, time 0.02 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000000, max 0.000000 (between atoms 1322 and 1324)
>> bonds that rotated more than 30 degrees:
>>  atom 1 atom 2  angle  previous, current, constraint length
>>    1360   1361   37.5    0.1010   0.1010      0.1010
>> [continues with more errors until Segmentation fault 11]
>>
>>
>> I have tried both constraints with a reduced and increased deltaStep
>> (0.2,0.02,0.002,0.0002) no change. I have also taken constraints off,
>>this
>> does work but then fails again when constraints are returned. I have
>>tried
>> both Steep and cg, both fail with the same result.
>>
>> The .mdp file I used (taken from the latest release of Justin¹s
>>tutorials)
>> is:
>> ; energy.mdp - used as input into grompp to generate em.tpr
>> ; Parameters describing what to do, when to stop and what to save
>> integrator      = steep         ; Algorithm (steep = steepest descent
>> minimization)
>> emtol           = 700.0        ; Stop minimization when the maximum
>>force
>> < 1000.0 kJ/mol/nm
>> emstep          = 0.002          ; Energy step size
>> nsteps          = 200000                ; Maximum number of
>>(minimization)
>> steps to perform
>>
>> ; Parameters describing how to find the neighbors of each atom and how
>>to
>> calculate the interactions
>> cutoff_scheme = verlet
>> nstlist         = 20            ; Frequency to update the neighbor list
>> and long range forces
>> ns_type         = grid          ; Method to determine neighbor list
>> (simple, grid)
>> rlist           = 1.4           ; Cut-off for making neighbor list
>>(short
>> range forces)
>> coulombtype     = PME           ; Treatment of long range electrostatic
>> interactions
>> rcoulomb        = 1.4           ; Short-range electrostatic cut-off
>> rvdw            = 1.4           ; Short-range Van der Waals cut-off
>> pbc             = xyz           ; Periodic Boundary Conditions (yes/no)
>>
>> ;ADDED THIS BIT MYSELF
>> continuation    = no               ; first dynamics run
>> constraint_algorithm = lincs    ; holonomic constraints
>> constraints     = h-bonds; all-bonds (even heavy atom-H bonds)
>>constrained
>> lincs_iter      = 1                         ; accuracy of LINCS
>> lincs_order     = 8                         ; also related to accuracy
>>
>>
>> The .pdb was generated using I-TASSER. I have tried refining the
>>hydrogen
>> placement via -ignh during pdb2gmx, and I also tried ³Protein
>>Preparation²
>> (bond ordering - again, hydrogen bond placement) in Schrodinger. All the
>> same.
>>
>> I was hoping that I could actually watch a rough-and-ready minimisation
>> using Avogadro, however, the release I have keeps crashing whilst trying
>> to open large structures.
>>
>> Any suggestions on what I could try next?
>>
>
>All signs point to unreasonable starting structure.  How about minimizing
>the 
>protein alone, in vacuo?  Maybe restrain the backbone and try to minimize
>side 
>chains, then in the absence of any restraints?
>
>-Justin
>
>-- 
>==================================================
>
>Justin A. Lemkul, Ph.D.
>Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
>Department of Pharmaceutical Sciences
>School of Pharmacy
>Health Sciences Facility II, Room 629
>University of Maryland, Baltimore
>20 Penn St.
>Baltimore, MD 21201
>
>jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>http://mackerell.umaryland.edu/~jalemkul
>
>==================================================
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