Hi Justin,
No. I have not added any ions.
Samrat
________________________________
From: Justin A. Lemkul <jalem...@vt.edu>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Sent: Friday, October 21, 2011 11:39 AM
Subject: Re: [gmx-users] mismatch in coordinate and topology
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
========================================
-- gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or
send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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
========================================
-- gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or
send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
