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:
popc.mdp
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
popc.top
#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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