[gmx-users] mismatch in coordinate and topology

Samrat Pal psamrat10 at yahoo.com
Fri Oct 21 17:59:26 CEST 2011

Hi Justin,
(1) None of the ligands have 31 atoms - FAD has 86 atoms and MHF has 54 atoms. The error msg. does not show any specific mismatching.
(2) I forgot to mention that I have increased the number of the atoms on the top (2nd line) of the gro file after adding the 2 ligands.

From: Justin A. Lemkul <jalemkul at vt.edu>
To: Samrat Pal <psamrat10 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Friday, October 21, 2011 8:49 AM
Subject: Re: [gmx-users] mismatch in coordinate and topology

Samrat Pal wrote:
> Hi All,
>          I am trying to minimize the chryptochrome structure that has one FAD and one MHF ligand bound to it.
> Following are the steps that I performed ----
>  (1) Created the protein coordinate(gro) file using pdb2gmx command and choosing GROMOS43a1 force-field
>  (2) Created the FAD and MHF topology and coordinate files using PRODRG where I have chosen
> a) no chirality, b) full charge and (c) no minimization. /I have not seen any option for choosing force-field in the server/.  (3) I have taken the corresponding coordinate and topology files from that server, appended the coordinates of both the ligands in the gro file of the protein (before the box vector i.e. the last line), and also included the ligand topology files in the topol.top file after "posre.itp" and before "spc.itp"accordingly.

Regarding (2) and (3) - the output of the PRODRG server will likely give poor results.  See the paper linked from http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips.

>  (4) I have also added two lines in the [molecules] section like,
> FAD  1
> MHF  1
>  (5) Then I have created a cubic box where I have taken the coordinate and solvated the protein+ligands coordinate with spc water model using genbox.

A dodecahedral box is likely going to be more efficient, but this is not relevant to the problem at hand.

> (6) Then I tried to create the em.tpr file from em.mdp file using grompp command.
>  I got the following error message --- number of atoms in the coordinate file does not match with topology file where topology file has 31 missing atoms according to the numbers shown in the error message.

OK, so do any of your molecules consist of 31 atoms?  Do you get any notes about non-matching names?

> I have checked the topology file after solvation and it is updated having the last line of the file with SOL  34741.
>  I have been using gromacs for few months and I have successfully simulated systems with ligands before. Could anybody please tell me where I am doing wrong?  

Did you properly increment the number of atoms in the coordinate file after adding your ligands?


-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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