[gmx-users] Gro file does not match topology

Sotirios Dionysios I. Papadatos si.papadatos at edu.cut.ac.cy
Fri Jan 27 06:52:21 CET 2017

OK, dividing the number by 3 could be used if you are using a 3-point water solvent. Apart from that, assuming that during the procedure up to minimization you didn't forget to update your topology file, this usually comes up if you manually edit your .gro, .top files. Check your .gro file, top left corner you can see the number of atoms, then verify in your topology file (bottom) that the number of molecules (time their atoms) sum up to the same number. If not, we'll need more info.

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Poncho Arvayo Zatarain <poncho_8629 at hotmail.com>
Sent: Thursday, January 26, 2017 7:56:07 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Gro file does not match topology

Hello gromacs users: I´m trying to do a minimization with 26 dppc 230 dppe 8960 water and 72 molecules of a compound. But when i used grompp the following error appears: gro file (58674) does not match with top file (58666). Also i tried with 8961 molecules of solvent and the same error appears gro (58674) top (58669), 8962 solv gro (58674) top (58672), 8963 solv gro (58674) top (58675) and 8964 molecules of solvent and the same error appears with gro file (58674) and top file (58678). What can i do in this case? I read in the forum about divided the number by 3 but i don´t know how.

My top is


DPPE 230

Compund 72

Water 8960

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