[gmx-users] error... plz help

nikhil damle pdnikhil at yahoo.co.in
Fri Jul 11 15:36:47 CEST 2008

Dear all ,

I am trying to run energy minimisation of a modified PDB file (part of ATOM block copy-pasted in dummy.pdb file)

it has number of missing atoms (in the original pdb file itself) . hence the .top file is created with option "-missing".

as it has charge of -2, i have added 2 Na+ ions to .top file by replacing 2 solvent molecules. now when i try to re compile the grompp, it says that the earlier formed .tpr file (co-ordinate file for compiling grompp after adding ions) and the new .top file have different number of co-ordinates.

How should i resolve the problem ??
plz help as soon as possible.

one of the gms-users in need

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