[gmx-users] number of coordinates ... does not match - 55 coordinates too much

[Volker Wirth]

Hi all,

so this ist yet another question concerning this error message, but I
searched the archive/wiki and tried out very much (incl. dos2unix *),
so I write to the list myself and hope, someone has an idea:

I set up a system consisting of 110 molecules lipids (à 46 atoms), a
peptide (187 atoms) and 6868 water molecules (à 3 atoms)
--> I have 25851 atoms calculationally and this is also what my .pdb tells me.

My topology contains:

-------------------------------------------------------
#include "ffG53a6.itp"
#include "lipid.itp"
#include "protein.itp"

;water
#include "spc.itp"

[ system ]
; Name
110 lipids + protein + water

[ molecules ]
; Compound        #mols
Protein        1
Lipid            110
SOL             6868
-------------------------------------------------------

So the compounds seem to be correct.

If I execute grompp, it tells me, that there are 55 coordinates too
much in the topology:

-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: grompp.c, line: 448

Fatal error:
number of coordinates in coordinate file (solvated.pdb, 25851)
             does not match topology (topol_solvated.top, 25906)
-------------------------------------------------------

I cannot find out, where 55 coordinates should come from!

Did anyone encounter such a problem before and can tell me what the reason is?
Thanks and have a nice weekend

Volker
-- 
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Volker Wirth
Center for Medical Physics and Technology
Biophysics Group
FAU Erlangen-Nuremberg

Email: vwirth%at%biomed.uni-erlangen.de
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