[gmx-users] Series of questions
feenstra at chem.vu.nl
Thu Sep 18 08:52:04 CEST 2003
Raj Badhan wrote:
> I have a few questions that I hope someone can answer.
> OK, my system is setup in windows xp.
> I'm running a simulation on a protein within a water box, using
> gromacs force fields.
> I can get upto the point of where I have added the water and am
> beginning a position restrained MD simulation.I pre-processes the
> pr.mdp file (laid out as in the John Kerrigan tutorial except for an
> extra entry for a Cl counter ion).
> At this point I get a number of errors:
> system has non-zero total charge 1.80000000e+0.01.
> I had to add a Cl counterion to balance up the +1 charge on the
> protein and dont understand why this error has occured.
Well, clearly, because you still have a +18 charge somehow. Did you
check you topology file? The pdb2gmx generated topologies keep a
cumulative sum of charge after the atoms (in [atoms] section), so you
can see at the end what the total charge on the protein is, and you
could find out if it goes wrong on some specific residue.
If I understand you correctly, you have 1 protein, waters, and 1 ion?
Does your [molecules] section look like?:
[ molecules ]
> and also, i get a error saying:
> Fatal error:...no. of co-ordianted in co-ord. file doesnt match the
> topology file.
> Now, I corrected the TOP file by removing one water and adding the
> entry for the Cl ion and adding ions.itp in the relevant place, and
> again, I dont understand why this error occurs.
Mis-counting occurs easily, especially after repeated modifications of
the files... Check if the protein has the right size, count waters e.g.
by 'grep "OW" conf.gro | wc -l' (OW is the water Oxygen, wc -l counts
> When we add the counterion, according to the John Kerrigan
> tutorial, he has his output file from genion called fws_ion.gro.
> Sould I be using this file (myprotein_ion.gro) to continue onto the
> energy minimisation and position-restrained sections?
I'd say yes, why else (and where else?) would you have added the ion?
> I'd really appreciate any help as this is bugging the hell out of me!
> I'd also like to be able to e-mail someone who could assit me
> through this stage of my simulations when required rather then
> sending endless e-mail to this message board and clogging up
> your servers.
You could ask the author of the tutorial, he should be familiar with
the specifid choices of how the different steps are executed...
> Hope some good soul out there can lend a hand.
Hope this helped... :)
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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