[gmx-users] mismatch in coordinate and topology

Justin A. Lemkul jalemkul at vt.edu
Fri Oct 21 17:49:14 CEST 2011

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 

> (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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