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

Vitaly Chaban vvchaban at gmail.com
Sat Oct 11 20:05:46 CEST 2008

gurgo> I want to perform MD Equilibration run under position restrained for
gurgo> 200ps. Bond
gurgo> distances were constrained using the LINCS (Linear Constraints) algorithm,
gurgo> the water molecules were restrained using the SETTLE algorithm. In order to
gurgo> do this I have modified nsteps in original pr.mdp file. Following is the
gurgo> modified file contents:
gurgo> Then I wanted to do grompp with this modified pr.mdp file. But it is showing
gurgo> a Fatal error like,
gurgo> Fatal Error:
gurgo> number of coordinates in coordinate file does not match topology.

gurgo> But if I use the original pr.mdp (without modifying it for 200ps) the grompp
gurgo> runs properly. I am not understanding what to do now. Please help me out.

Please tell us all the actions you performed especially the tool you
use for modifying .mdp. It seems the problem is
in file formats...

Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua
skype: vvchaban
tel.: +38-097-8259698

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