[gmx-users] grompp error

[chris.neale at utoronto.ca]

> 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