[gmx-users] cpp error again

[David van der Spoel]

On Wed, 2003-07-02 at 06:50, Y U Sasidhar wrote:
> 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

[l1:~] % which cpp
/usr/bin/cpp

replace it with the answer you get from this command

> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> 
> 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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