[gmx-users] grompp error

pragya chohan pragyachohan at hotmail.com
Tue Oct 9 20:08:15 CEST 2007

hi... i have been trying to do grompp for the following file but am getting this error:
There were 1 error(s) processing your inputWARNING 3 [file "popc.top", line 32]:  7380 non-matching atom names  atom names from popc.top will be used  atom names from popc.pdb will be ignored
double-checking input for internal consistency...ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist.There were 3 warnings
The grompp command i am using is:
grompp -f 7eq_w.mdp -c popc.pdb -p popc.top -o poc.tpr
the inputs are:
title                = popc128aintegrator           = mddefine               = -DPOSRES -DFLEX_SPCdt                   = 0.002nsteps               = 25000nstxout              = 500ns_type              = gridpbc                  = xyzconstraints          = hbondsconstraints_algorithm= shakecoulombtype          = PMEvdwtype              = cut-offrcoloumb             = 1.4
Tcoupl               = berendsenpcoupl               = berendsentau_t                = 0.1       0.1tc_grps              = POPC      SOLref_t                = 300       300ref_p                = 1.0pcoupltype           = isotropiccompressibility      = 4.5e-5gen_temp             = 300
#include "ffgmx.itp"#include "lipid.itp"#include "popc.itp"
#ifdef FLEX_SPC#include "flexspc.itp"#else#include "spc.itp"#endif
#ifdef POSRES_WATER; Position restraint for each water oxygen[ position_restraints ];  i funct       fcx        fcy        fcz   1    1       1000       1000       1000#endif
; Include generic topology for ions#include "ions.itp"
#ifdef POSRES#include "lipid_posre.itp"#endif
[ system ]; NamePure DPPC bilayer with 128 lipids and 3655 water molecules
[ molecules ]; Compound        #molsPOPC              128SOL               2460
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