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.
Samrat
________________________________
From: Justin A. Lemkul <jalem...@vt.edu>
To: Samrat Pal <psamra...@yahoo.com>; Discussion list for GROMACS users
<gmx-users@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
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