[gmx-users] (no subject)

chris.neale at utoronto.ca chris.neale at utoronto.ca
Fri May 12 08:48:46 CEST 2006

Your reported errors:
>1..while running  pdb2gmx
>   warning :'FE2' not found in residue topology database...

What force field are you using in pdb2gmx? look at that .itp file and the files 
that it includes (.itp file is prefaced by 'ff' and is in share/gromacs/top/ or 
similar directory)
If you can't get pdb2gmx to work then get rid of your Iron from the PDB and run 
pdb2gmx to get the .gro and then add the iron back into the .gro (pdb2gmx seems 
to work easily only with pure protein files, although perhaps a more experienced 
user can get it to work with anything).
Regardless, it is key to know what your force field is calling the iron2 atom.

>2..when i'm trying to run grompp
>   Note: System has non-zero total charge : -6.000002e+00.
>   is it necessary to neutralise the charge, if so genion 
>   has to run Na means how much i've to add..ie how to calculate it...

You must have a charge neutral system to use Ewald/PME/etc... If you are using a 
pure cutoff or 2-step cutoff then a net negative charge should be fine (as long 
as your cutoff values are otherwise acceptable). I am not sure what your 2nd 
question is here??? Add 6 positive monovalent ions to neutralize.

>3..with the avialable output file i tried to run mdrun..
>   showing the error that can not open File toplo.tpr but my tpr file is
>   out3.tpr.i'm giving correctly in command also like mdrun -s out3 
>   -o out4 -c out4 -v

First of all, forget about mdrun until you solve the other problems. How do you 
run grompp successfully if you have problems with pdb2gmx? Regardless, try -s 
out3.tpr (add the .tpr) although I can't imagine that that will help. It appears 
that your -s argument is not getting read... look for errors/warning before the 
one that you mentioned.
Hope that helps.

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