[gmx-users] energy minimisation - LINCS WARNING

Mark Abraham mark.j.abraham at gmail.com
Mon Oct 3 13:03:47 CEST 2016


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
> >
> >==================================================
> >--
> >Gromacs Users mailing list
> >
> >* Please search the archive at
> >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >posting!
> >
> >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> >* For (un)subscribe requests visit
> >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >send a mail to gmx-users-request at gromacs.org.
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.


More information about the gromacs.org_gmx-users mailing list