Fw: [gmx-users] number of coordinates in coordinate file does not match topology

[Acoot Brett]

Dear All,
 
The problem really occurs in the ion addition step.
 
In order to keep 0.1 M ion concentration, 20 Na+ and 20 C1- were added. In order to keep 0 charge, 8 Cl- were added.
 
From the .gro file, 48 water (72 H and 48 O) were deleted in order to add the 38 charges, which makes there was a 96 atom reduction.
 
For the top file, we modify it in the following way, 48 SOLs were deleted, 20 Na+ were added, and 28 Cl- added.
 
In the above manner, however, it indicated the " number of coordinates in coordinate file (1LW9-EM-solvated.gro, 32748) does not match topology (1LW9.top)".
 
Thus how do we modify the .gro file and the .top file so that the number of coordinated will be equal between them?
 
Cheers,
 
Acoot  

________________________________
 From: Justin A. Lemkul <jalemkul at vt.edu>
To: Acoot Brett <acootbrett at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Monday, 19 March 2012 12:06 PM
Subject: Re: [gmx-users] number of coordinates in coordinate file does not match topology 
   


Acoot Brett wrote:
> Dear All,
>  I am practicing the on-line tutorial http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/.
>  In the step "mdrun -v -deffnm 1LW9-EM-solvated" of "Energy minimization of the solvated system", it says "
> Converged to machine precision  , but not to the requested precision Fmax < 1". Before this step, all the other steps run fine.
>  In the step "grompp -v -f pr.mdp -c 1LW9-EM-solvated.gro -p 1LW9.top -o 1LW9-PR.tpr" of "Relaxation of solvent and hydrogen atom positions:
 Position restrained MD", it says "
> Fatal error:  number of coordinates in coordinate file (1LW9-EM-solvated.gro, 32748) does not match topology (1LW9.top, 0)"
>   I am looking forward to getting a reply from you on how to what leads to the error message.
>  

http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology

You need to make sure the contents of the [molecules] directive always matches that of the coordinate file, in terms of the number of molecules and the order in which they are present.

-Justin

-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg,
 VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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