[gmx-users] Use of restraints gives segmentation fault

[XAvier Periole]

On May 13, 2010, at 3:58 PM, XAvier Periole wrote:

>
> Why don't you simply define a extra bond between your two CYS side  
> chains beads?
Sorry, I red to quick ...

>
> On May 13, 2010, at 3:31 PM, Anna Duncan wrote:
>
>>
>> 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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>
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