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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