Fw: [gmx-users] number of coordinates in coordinate file does not match topology
acootbrett at yahoo.com
Mon Mar 19 06:39:35 CET 2012
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?
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.
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 A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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