[gmx-users] error... plz help

Justin A. Lemkul jalemkul at vt.edu
Fri Jul 11 15:53:39 CEST 2008

Quoting nikhil damle <pdnikhil at yahoo.co.in>:

> 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".

Be careful with doing this!  If you have a broken molecule, your topology may
not be accurate!

> 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.

Exact command lines and exact output are greatly preferred to your
interpretation of the problem.  Why are you feeding grompp a .tpr file, anyway?
 Its purpose is to create a .tpr file.

Have a look at the following:


Doing a thorough search of the list archives and wiki site will often lead you
to a solution for errors experienced by new users.  Also, please choose an
appropriate subject line to your emails in clear English.  Subjects like yours
often get shifted to the "trash" pile of an individual who would otherwise
probably have good ideas :-)


> How should i resolve the problem ??
> plz help as soon as possible.
> Regards,
> one of the gms-users in need
>       Meet people who discuss and share your passions. Go to
> http://in.promos.yahoo.com/groups/bestofyahoo/


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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