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 <[email protected]>
To: Acoot Brett <[email protected]>; Discussion list for GROMACS users
<[email protected]>
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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