[gmx-users] Error prb

[Tsjerk Wassenaar]

Pay attention Anton!

There are fourteen atoms *more* in the .gro file than in the .top file, 
not the other way around.

>> Fatal error: number of coordinates in coordinate file
>> (1HRC_b4pr.gro, 10243)
>>              does not match topology (1HRC.top, 10229)


Anton Feenstra wrote:

> Xavier Periole wrote:
>
>>
>> That is a simple one: the number of atoms defined in your topology
>> file (topol.top) is different from the number of atoms that are your
>> conf.gro. You have 14 atoms extra in the conf.gro that are not in the
>> topology file. Check the missing atoms and include them in the
>> topology file.
>
>
> Yes, this is probably due to using genion. It has replacesd 7 waters with
> 7 Cl-, which leaves you 14 atoms short. Subtract 7 waters from the 'SOL'
> line in your .top file, and add a line for 7 Cl-.
>
>


-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) 	Tsjerk A. Wassenaar, M.Sc.
-- :) 	Molecular Dynamics Group
-- :) 	Dept. of Biophysical Chemistry
-- :) 	University of Groningen
-- :) 	Nijenborgh 4
-- :) 	9747 AG Groningen
-- :) 	The Netherlands
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) 	Hi! I'm a .signature virus!
-- :) 	Copy me into your ~/.signature to help me spread!
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~