[ intermolecular_interactions ] with [ distance_restraints ] / [ bonds ] not working - Redmine #2953
Archive from user: Eiso AB
see also https://mailman-1.sys.kth.se/pipermail/gromacs.org\_gmx-users/2019-May/125277.html
I’m trying to implement NMR (noe) and Hbond restraints between protein,
ligand and 2 SOL molecules
using [ distance_restraints ] (or [ bonds ])
[ intermolecular_interactions ]
[ distance_restraints ]
; ai aj ftype label rtype low up0 up1 weight ; & source
1607 5241 1 18 1 0.5680 0.5680 0.6384 1 ; # 120 leu hd1# 411 lig h09
5.68 # 4.74 0.94
1608 5241 1 18 1 0.5680 0.5680 0.6384 1 ; #
1609 5241 1 18 1 0.5680 0.5680 0.6384 1 ; #
…etc
[ bonds ]
5261 5569 10 0.2800 0.3200 10.4333 1 ; # 411 lig o19 501 sol ow 3.00
etc…
With both [ bonds ] and [ distance_restraints ] the mdrun starts, but non of the restraints seem to be active - waters just fly away etc.
Also for [ distance_restraints ] no Dist. Res energy is printed in the log file - unlike when they intramolecular and defined with the appropriate molecule section.
Not sure if it is related, but when I run gmx_disre I get the following error:
%>gmx disre -s md_0_10.tpr -f md_0_10.xtc
Program: gmx disre, version 2019-beta1
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
and
%>gmx nmr -s md_0_10.tpr -f md_0_10.edr -viol viol.xvg
yields:
Program: gmx nmr, version 2019-beta1
Source file: src/gromacs/commandline/filenm.cpp (line 88)
Function: opt2fn(const char**, int, const t_filenm**)::__lambda1
Assertion failed:
Condition: false
opt2fn should be called with a valid option
If needed I can produce a toy example but will have to make one
up since I can’t share the files I’m working on -let me know.
Eiso
(from redmine: issue id 2953, created on 2019-05-14 by gmxdefault, closed on 2019-05-29)
- Changesets:
- Revision 3cbf2eb5 by Berk Hess on 2019-05-29T15:59:54Z:
Fix missing intermolecular interactions with DD
When running with domain decomposition, all intermolecular interactions
(when present) were ignored.
Fixes #2953
Change-Id: I98783f4175b40fdfa6ad035323e0897e8caaee5c
- Revision 9e4323b6 by Berk Hess on 2019-08-02T14:50:54Z:
Made gmx disre work with non-consecutively labeled restraints
gmx disre assumed restraint were consecutively labeled starting at 0.
Refs #2953
Change-Id: I7d9c14d43854c88cb1cdec89fc297c64cbea8783
- Uploads:
- topol.top
- conf.gro
- grompp.mdp
- test-1.log mdrun log file for run that works ok.
- test-2.log mdrun log file for broken run