[gmx-users] cpp error again

[Y U 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
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

replace the line cpp = /lib/cpp by something else appropriate for your
system. If necessary install a compiler.
============================
I have reinstalled cpp rpm ( I had to use --force option ); Still the 
problem persists. On another xeon with same versions of RH 8.0 and gmx 
and same peptide files this problem does not occur at all. Do you advise 
  me to reinstall linux all over again ? ( I have already reinstalled 
gromacs again; the problem is still present )

> 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
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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