[gmx-users] Use of restraints gives segmentation fault

[Anna Duncan]

I'm trying to energy minimise a protein structure.  In one area of the  
structure there are some salt bridges and when I do an energy  
minimisation without any restraints these are disrupted, which is  
something I want to avoid.  To that end, I've tried restraining the  
residues that are involved, first with position restraints and then  
with distance restraints, but in both cases I get a segmentation fault  
in the same place.
The command I issue looks like:
grompp -f em.mdp -c 1okc_ex.cg.gro -p 1okc_ex.top -o 1okc_min_sbRes -v  
-n salt_bridges.ndx

and the output:
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Replacing old mdp entry 'unconstrained_start' by 'continuation'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.10#
checking input for internal consistency...

NOTE 1 [file em.mdp, line unknown]:
   For energy conservation with switch/shift potentials, rlist should  
be 0.1
   to 0.3 nm larger than rcoulomb.


NOTE 2 [file em.mdp, line unknown]:
   For energy conservation with switch/shift potentials, rlist should  
be 0.1
   to 0.3 nm larger than rvdw.

processing topology...
Generated 0 of the 465 non-bonded parameter combinations
Segmentation fault

--------------------------------------------------------------------------------------

Like I say, when I do this without the restraints, grompp and mdrun  
run fine.  The only differences, then, between the input is the line  
in em.mdp:
define = -DDISTRESB

The topoolgy file, 1okc_ex.top looks like:
#include "martini_v2.1.itp"
#include "1okc_ex.itp"
#ifdef POSRESB
#include posre_saltbridges.itp
#endif
#ifdef DISTRESB
#include distre_sb.itp
#endif

[ system ]
1OKC_EX SIMULATION

[ molecules ]
Protein 1

--------------------------------------------------------------------------------------

The position restraints file looks like:
; position restraints for r_28_r_31_r_133_r_136_r_230_r_233 of God  
Rules Over Mankind, Animals, Cosmos and Such

[ position_restraints ]
;  i funct       fcx        fcy        fcz
   52    1       1000       1000       1000
   53    1       1000       1000       1000
   59    1       1000       1000       1000
   60    1       1000       1000       1000
   61    1       1000       1000       1000
  296    1       1000       1000       1000
  297    1       1000       1000       1000
  303    1       1000       1000       1000
  304    1       1000       1000       1000
  305    1       1000       1000       1000
  505    1       1000       1000       1000
  506    1       1000       1000       1000
  511    1       1000       1000       1000
  512    1       1000       1000       1000
  513    1       1000       1000       1000

--------------------------------------------------------------------------------------

and the distance restraints file looks like:
; distance restraints for h1-h3_sb of God Rules Over Mankind, Animals,  
Cosmos and Such

[ distance_restraints ]
;   i     j ? label      funct         lo        up1        up2      
weight
    53   395 1     0          1    2.00181    2.20181     
3.20181          1
   297   513 1     0          1   0.462702   0.662702      
1.6627          1
    61   506 1     0          1     0.3818     0.5818      
1.5818          1

--------------------------------------------------------------------------------------


I can't work out what is giving the segmentation fault because I think  
the restraint files are in the right format and I can't think of what  
else would go wrong at this stage for a segmentation fault to occur.

In the grompp run that works (without any restraints) the line after  
where the segmentation error occurs in the other cases looks like:
Excluding 1 bonded neighbours molecule type 'Protein'

Many thanks,
Anna

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