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

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Mar 19 07:41:08 CET 2012

Hi Acoot,

Read the tutorial. It's explained there... Mind that that tutorial was
written for an earlier version of Gromacs and some things have changed. The
names of ions, for instance.



On Mar 19, 2012 6:40 AM, "Acoot Brett" <acootbrett at yahoo.com> wrote:

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

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

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