[gmx-users] nmr distance restraints
Eiso AB
eisoab at gmail.com
Tue May 14 11:05:25 CEST 2019
Hi David,
Happy to submit a report, but the site asks for a login/pw, which I don't
think I have.
E
On Tue, May 14, 2019 at 6:58 AM David van der Spoel <spoel at xray.bmc.uu.se>
wrote:
> Den 2019-05-13 kl. 18:42, skrev Eiso AB:
> > Hi again,
> >
> > one more piece of info. If I move the subset of restraints that are
> > intra-protein into a separate
> > [ distance_restraints ] section just after inclusion of the ligand
> topology
> > and run that , the dist.rest energies
> > and violation start appearing in the log file - so the dist. rest.
> section
> > itself seems to be ok.
> >
> > Still the dist. restraints in the [ intermolecular_interactions ] appear
> > to be ignored
> >
> > However gmx disre now complains that all parameters should be consecutive
> > Error message:
> >
> > Source file: src/gromacs/listed-forces/disre.cpp (line 174)
> > Function: init_disres(FILE*, const gmx_mtop_t*, t_inputrec*, const
> > t_commrec*, const gmx_multisim_t*, t_fcdata*, t_state*,
> gmx_bool)::__lambda0
> > Assertion failed: Condition: type_max - type_min + 1 == dd->nres
> > All distance restraint parameter entries in the topology should be
> > consecutive
> >
> Please submit a report on http://redmine.gromacs.org
> >
> > any help appreciated!
> > best,
> > Eiso
> >
> > E
> >
> >
> >
> > On Mon, May 13, 2019 at 2:49 PM Eiso AB <eisoab at gmail.com> wrote:
> >
> >> Hi,
> >> I've setup an mdrun with [ distance restraints ] but the restraints
> don't
> >> seem to have any effect on the simulation, so I'm wondering if there's
> >> anything i need to do to switch them on that I missed.
> >>
> >> gmx disre or gmx nmr doesn't give any info about restraints.
> >> and the .log file doesn't show any energy component for Distance
> >> Restraints, e.g.
> >>
> >> Energies (kJ/mol)
> >> Bond Angle Proper Dih. Ryckaert-Bell. Improper
> Dih.
> >> 4.14550e+03 1.13252e+04 1.29502e+04 9.20032e+01
> 6.00131e+02
> >> LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul.
> recip.
> >> 5.01723e+03 6.08476e+04 3.13964e+05 -2.12124e+06
> 5.15532e+03
> >> Potential Kinetic En. Total Energy Conserved En.
> Temperature
> >> -1.70714e+06 2.85181e+05 -1.42196e+06 -1.34064e+06
> 2.99828e+02
> >> Pressure (bar) Constr. rmsd
> >> 1.15517e+02 4.10744e-06
> >>
> >> I have defined restraints between protein, ligand and a few waters - all
> >> in different [molecules]
> >> - so I used [ intermolecular_interactions ] followed by [
> >> distance_restraints ]
> >>
> >>
> >> my topol.top ends like this :
> >>
> >> [ system ]
> >> ; Name
> >> Protein in water
> >>
> >> [ molecules ]
> >> ; Compound #mols
> >> Protein_chain_A 1
> >> lig 1
> >> SOL 35926
> >> NA 4
> >>
> >> [ intermolecular_interactions ]
> >>
> >> [ distance_restraints ]
> >> ; ai aj type index type' low up1 up2 fac ; # source
> >> 465 564 1 0 1 0.2540 0.2540 0.4115 1 ; # 308 ile hd+ 216 val
> >> hg1+ 2.54
> >> 465 565 1 0 1 0.2540 0.2540 0.4115 1 ; #
> >> 465 566 1 0 1 0.2540 0.2540 0.4115 1 ; #
> >> 466 564 1 0 1 0.2540 0.2540 0.4115 1 ; #
> >> 466 565 1 0 1 0.2540 0.2540 0.4115 1 ; #
> >> 466 566 1 0 1 0.2540 0.2540 0.4115 1 ; #
> >> 467 564 1 0 1 0.2540 0.2540 0.4115 1 ; #
> >> 467 565 1 0 1 0.2540 0.2540 0.4115 1 ; #
> >> 467 566 1 0 1 0.2540 0.2540 0.4115 1 ; #
> >> [...snap...]
> >> 1607 5241 1 34 1 0.5680 0.5680 0.6384 1 ; # 170 leu hd1# 411 lig
> h09
> >> 5.68
> >> 1608 5241 1 34 1 0.5680 0.5680 0.6384 1 ; #
> >> 1609 5241 1 34 1 0.5680 0.5680 0.6384 1 ; #
> >> [ ..snap ... ]
> >> 2720 5571 1 52 2 0.1900 0.1900 0.2900 1 ; # 217 asp od1 501 sol
> hw2
> >> 1.90
> >> 2720 5569 1 53 2 0.3000 0.3000 0.4000 1 ; # 217 asp od1 501 sol ow
> >> 3.00
> >>
> >>
> >> disre is set to simple. From the mdout.mdp
> >>
> >> []$ grep disre mdout.mdp
> >>
> >> ; Distance restraints type: No, Simple or Ensemble
> >> disre = Simple
> >> ; Force weighting of pairs in one distance restraint: Conservative or
> Equal
> >> disre-weighting = Conservative
> >> ; Use sqrt of the time averaged times the instantaneous violation
> >> disre-mixed = no
> >> disre-fc = 1000
> >> disre-tau = 0
> >> ; Output frequency for pair distances to energy file
> >> nstdisreout = 100
> >>
> >>
> >> gmx dump shows that the run topology has the distance restraints and
> looks
> >> ok to me
> >>
> >> gmx dump -s md_0_10.tpr |grep -10 dis
> >>
> >> [..snap..]
> >> Reading file md_0_10.tpr, VERSION 2019-beta1 (single precision)
> >> Reading file md_0_10.tpr, VERSION 2019-beta1 (single precision)
> >> disre = Simple
> >> disre-weighting = Conservative
> >> disre-mixed = false
> >> nstdisreout = 100
> >> 0 type=1038 (DISRES) 464 563
> >> 1 type=1038 (DISRES) 464 564
> >> 2 type=1038 (DISRES) 464 565
> >> 3 type=1038 (DISRES) 465 563
> >> 4 type=1038 (DISRES) 465 564
> >> 5 type=1038 (DISRES) 465 565
> >> [..snap ...]
> >> D.R.Viol. (nm):
> >> nr: 0
> >> [...snap...]
> >>
> >> functype[1038]=DISRES, label= 0, type=1, low=
> 2.54000008e-01,
> >> up1= 2.54000008e-01, up2= 4.11500007e-01, fac= 1.00000000e+00)
> >> functype[1039]=DISRES, label= 1, type=1, low=
> 2.56999999e-01,
> >> up1= 2.56999999e-01, up2= 4.12600011e-01, fac= 1.00000000e+00)
> >> functype[1040]=DISRES, label= 2, type=1, low=
> 3.72999996e-01,
> >> up1= 3.72999996e-01, up2= 4.80199993e-01, fac= 1.00000000e+00)
> >> functype[1041]=DISRES, label= 3, type=1, low=
> 3.84000003e-01,
> >> up1= 3.84000003e-01, up2= 4.88200009e-01, fac= 1.00000000e+00)
> >> functype[1042]=DISRES, label= 4, type=1, low=
> 2.33999997e-01,
> >> up1= 2.33999997e-01, up2= 4.04900014e-01, fac= 1.00000000e+00)
> >> functype[1043]=DISRES, label= 5, type=1, low=
> 2.39999995e-01,
> >> up1= 2.39999995e-01, up2= 4.06699985e-01, fac= 1.00000000e+00)
> >> functype[1044]=DISRES, label= 6, type=1, low=
> 3.03000003e-01,
> >> up1= 3.03000003e-01, up2= 4.35000002e-01, fac= 1.00000000e+00)
> >>
> >> etc...
> >>
> >> Any suggestions about what is wrong here would be appreciated
> >> Thanks,
> >>
> >> Eiso
> >>
> >>
> >>
> >>
> >>
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
> --
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