[gmx-users] problem during inflatgro process

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Apr 15 09:30:44 CEST 2009

Hi Nitu,

First of all, please try to use proper english for communication. This
way 'u don't make it EC-r 4 us'.
Second, you'd be better off getting some understanding of how
topologies and coordinate files are put together before trying to do
these things. A question like 'can I remove something from an .itp
file' is on the verge of being absurd. Of course you can. You just
have to make sure that you know what you are doing.

> [ molecules ]
> ; Name            number
> Protein_A           1
> Protein_B           1
> DMPC              119
> only the .itp file is present for protein and lipid

If you only have Protein(A,B) and DMPC in your system, then probably
the number of DMPC molecules is not what GROMACS sees in the topology
file (119). Check how many DMPC molecules are in your coordinate file
and decrease the numebr of DMPC molecules in the topology file.
However, I would strongly recommend doing some more reading first and
get some grips on the topology (file) format. Probably it wouldn't
hurt to follow some more tutorial material.



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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