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 <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
========================================
--
========================================
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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