[gmx-users] energy minimisation - LINCS WARNING
Nash, Anthony
a.nash at ucl.ac.uk
Mon Oct 3 13:08:28 CEST 2016
That’s a good suggestion, Mark. Will do :-)
Thanks
Anthony
Dr Anthony Nash
Department of Chemistry
University College London
Skeletal Tissue Dynamics Group
Committee member of London Matrix Group @LondonMatrixGrp
On 03/10/2016 12:03, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on
behalf of Mark Abraham" <gromacs.org_gmx-users-bounces at maillist.sys.kth.se
on behalf of mark.j.abraham at gmail.com> wrote:
>Hi,
>
>Sounds like you could check the output from that tool, and if it gave no
>warning (or offers you no way to choose another rotamer) then you could
>make some constructive feedback to its authors :-)
>
>Mark
>
>On Mon, 3 Oct 2016 11:22 Nash, Anthony <a.nash at ucl.ac.uk> wrote:
>
>>
>> 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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