[gmx-users] mismatch in coordinate and topology

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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