[gmx-users] nmr distance restraints
David van der Spoel
spoel at xray.bmc.uu.se
Tue May 14 06:57:53 CEST 2019
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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