[gmx-users] mismatch in coordinate and topology

[Justin A. Lemkul]

Samrat Pal wrote:
> 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.
>  

Did you add any ions after solvation?  And if so, did you update your topology? 
  If SOL is the last entry, then likely not.

-Justin

> Samrat  
> 
> *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
> 
> -- ========================================
> 
> 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
> 
> ========================================
> 
> 

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

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

========================================