[gmx-users] cpp exitcode 32512; grompp error

[Y. U. Sasidhar]

David van der Spoel wrote:

>replace the line cpp = /lib/cpp by something else appropriate for your
>system. If necessary install a compiler.
>
1. /lib/cpp exists on our RH8.0, dual xeon system on which we see this 
error.
2. on RH 7.x dual P3 we don't have this problem.
3. On our xeon system also with another student's mdp file which is not 
very different, grompp doe not complain for the same peptide system.
4. For another different peptide we don't have any problem with grompp 
on the same xeon system.
There may be problem with mdp file which we could not isolate.


>
>  
>
>>cpp exit code: 32512
>> betahair.top > grompp6gfnPT'top -DFLEX_SPC
>>' command is defined in the .mdp file
>>processing topology...
>>processing coordinates...
>>Fatal error: number of coordinates in coordinate file (solvation.gro, 6191)
>>             does not match topology (betahair.top, 0)
>>===================================
>>our_comment:( total number of atoms do match by visual inspection )
>>===========================
>>mdp file for em
>>==============================
>>cpp = /lib/cpp
>>define = -DFLEX_SPC
>>integrator = steep
>>nsteps = 300
>>emtol = 2000
>>emstep = 0.01
>>nstxout = 25
>>nstvout = 25
>>nstlist = 10
>>nstenergy = 25
>>nstcomm = 1
>>ns_type = grid
>>rlist = 1.5
>>rcoulomb = 1.5
>>rvdw = 1.5
>>rcoulomb_switch = 1.0
>>rvdw_switch = 0.9
>>coulombtype = shift
>>vdwtype = shift
>>Tcoupl = berendsen
>>tc_grps    = Protein SOL
>>tau_t    =   0.1     0.1
>>ref_t =     300     300
>>energygrps = Protein SOL
>>Pcoupl = no
>>gen_vel = no
>>gen_temp = 300
>>gen_seed = 173529
>>constraints = none
>>constraint_algorithm = lincs
>>    
>>


-- 
 Sasidhar