[gmx-users] mismatch in coordinate and topology
Justin A. Lemkul
jalemkul at vt.edu
Fri Oct 21 20:39:03 CEST 2011
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.
> *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
> > (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
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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