[gmx-users] Re: Genion and number of Ions (David van der Spoel)

Marc Saric marc.saric at mpi-dortmund.mpg.de
Wed Sep 25 19:23:23 CEST 2002

David van der Spoel wrote:

>> 2. Question: What to do with fractional charges (i.e. -3.2 ?)
> That is wrong. There must be an error in your topology.

I checked the input-pdb-file:

It consists of 3 protein-strands without modifications etc., one MG-ion 
and some waters (ligand has been removed before for separate processing).

To check for the error, I have split the file into two parts:


grompp reports a charge of +2 for Water+Ion as expected (Mg) but 
something weird for the protein (-2.39e+1).

I double-checked, that all atoms are there and that the termini are 
correctly "capped" with OXT-atoms, but still, conversion gives the 

Any explanation (beside "must be a broken pdb-file")?

Here are the commandlines:

pdb2gmx -f protein.pdb -p protein.top -sort -o protein.gro
grompp -v -f em.mdp -c protein.gro -o em -p protein.top

Here is the em.mdp (although this should not matter I think?):

title               =  protein
cpp                 =  /lib/cpp
define              =  -DFLEX_SPC
constraints         =  none
integrator          =  steep
dt                  =  0.002    ; ps !
nsteps              =  1000
nstlist             =  10
ns_type             =  grid
rlist               =  0.9
coulombtype             =  PME
rcoulomb            =  0.9
rvdw                =  0.9
fourierspacing          =  0.12
fourier_nx              =  0
fourier_ny              =  0
fourier_nz              =  0
pme_order               =  4
ewald_rtol              =  1e-5
optimize_fft            =  yes
;       Energy minimizing stuff
emtol               =  1000.0
emstep              =  0.01

Bye,  Marc Saric

Max-Planck-Institut fuer molekulare Physiologie
Otto-Hahn-Str.11  44227 Dortmund  phone:0231/133-2168

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