[gmx-users] Series of questions

Anton Feenstra feenstra at chem.vu.nl
Thu Sep 18 08:52:04 CEST 2003

Raj Badhan wrote:
> Hi,
> I have a few questions that I hope someone can answer.

I'll try!

> 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 ]
Protein		1
SOL		5127
Cl-		1

> 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

> Thirdly.
> 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 |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |

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