[gmx-users] Missing Residues are list ind pdb file

Pär Bjelkmar bjelkmar at cbr.su.se
Mon Jan 18 12:50:36 CET 2010


Note, that this is indeed the size of the charge groups in the CHARMM force field. You could run pdb2gmx -nochargegrp if you know what you're doing. 

Pär Bjelkmar

> I think the notes from grompp are pretty clear. You need to redivide  
> your charge groups so that they contain fewer atoms. You can do this  
> in the .top or .itp file and you can find out how to do that in the  
> manual. Feel free to post your original and charge-group-modified  
> topologies back here if you want people to take a look at them.
> Chris.
> -- original message --
> I am trying to equilibrate a POPC membrane with 128 POPC molecules, but
> grompp gives out the following notes and minimization with mdrun does not
> work. The output on screen of mdrun comes out like this:
> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  =  1.4422483e+17
> Maximum force     =            inf on atom 4082
> Norm of force     =            inf
> And grompp notes are:
> NOTE 2 [file topol.top, line unknown]:
>   The largest charge group contains 12 atoms.

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