[gmx-users] cpp exitcode 32512; grompp error

[Y. U. Sasidhar]

It seems the error is caused by file format of the mdp file.
Once the file format of the mdp file is changed to unix ( :se ff=unix in 
vim/gvim ) the problem disappeared.
Sasidhar

>On Mon, 2003-06-30 at 14:18, Y U Sasidhar wrote:
>  
>
>>We have encountered the following grompp error prior to energy 
>>minimization of a peptide in spc water using steep:
>>On archives also a few people reported this error, but no clear answer 
>>except that mdp file may  be badly created.
>>we tried to play with mdp file by adding , deleting lines etc but  to no 
>>avail.
>>What kind of error (in mdp file ? )  can cause this error ?
>>=============error message======================
>>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.10#
>>Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
>>checking input for internal consistency...
>>...ling /lib/cpp
>>: No such file or directory
>>

>>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
>>    
>>