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
Your topology is incorrect. I am hesitant to assist more because 1)
you didn't include your topology here, 2) there is a massive amount of
questions exactly like this one for lipid topology problems, and 3)
you do not appear to be helping yourself (see next section).
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
This means exactly what it says. Did you read this carefully? your
rcoulomb=1.4 therefore your box needs to be longer than 2.8nm, but
this error message is telling you that it is not. Therefore make your
box bigger. Try this:
editconf -f popc.pdb -o popc.gro
tail -1 popc.gro
--> here you see your box dimensions.
WARNING: don't make your box 2.8001nm since it will likely shrink a
little if you are doing constant pressure.
WARNING: did you even turn on constant pressure? I think not. However
you have set some variables for constant pressure ... this is not the
same as turning it on. Look at the mdp options for pressure coupling.
WARNING: Once you change your box size (the source of the error) then
grompp is going to allow you to continue past the warnings (the atom
names don't match). If your topology is still incorrect then your next
error will be about a 1-4 interaction that is larger than 1nm. But
that won't actually be the source of the problem... the source of the
problem is that your topology is incorrect.
SUGGESTION: make a simple test system with one lipid and one water and
no PBC. If you can go through grompp and a short mdrun then you can
have some measure of faith in your topology.
Chris.
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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