[gmx-users] nmr distance restraints

[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


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
>
>
>
>
>