[gmx-users] fit the secondary structure time serie graph in page

ABEL Stephane 175950 Stephane.ABEL at cea.fr
Fri Jan 18 11:53:26 CET 2008 

Thank you it works now

Stefane
> Hi gromacs users
>
> When I use the xpm2ps utility to made a ps graphic of the secondary structure
> with my xpm file, the graph obtained is show in portrait orientation and by
> consequence trucated because the page width is to small. How to change the
> orientation of graph with xpm2ps (for example a landscape orientation) to fit
> the graph in one page ?

I don't know about changing the orientation, but I know that the horizontal size
of the output .ps file can be altered using an .m2p file (-di option).  An
example of one can be found here:

http://www.gromacs.org/documentation/reference/online/m2p.html

Specifically, try decreasing the xbox value; I've had success with that.

-Justin

>
> Thanks for your response
>
> Stefane
> _______________________________________________
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========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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


------------------------------

Message: 4
Date: Thu, 17 Jan 2008 13:37:32 -0500
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] How to remove H atom from residue in gro
	file?
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <1200595052.478fa06c74553 at webmail.vt.edu>
Content-Type: text/plain; charset=ISO-8859-1

Quoting Nelson Cotrim <nhcotrim at gmail.com>:

> Hi gmx users,
> I am rather new to MD, Linux environment and almost everything related
> to it. I am a geneticist working on mutations, so please, keep it
> simple :)
> This may be trivial and there may be an answer on the list already,
> but I do not even know how to search for it - the way I tried did not
> return anything useful.

http://www.gromacs.org/component/option,com_wrapper/Itemid,165/

Make sure the 'Mailing List' box is checked.

> I am analysing a mutation in a binding domain of a protein, and the
> ligand is phosporylated (a SER). I tried to use ff43a1p but kept
> getting errors in the FF files (hdb, rtp, etc), so instead I am used
> PRODRG to parametrize the PO4 (PO3+OG), changed the SEP to SER in the
> PDB file and then edited the .gro and .top files adding the data for
> the PO3.

Using the beta version of PRODRG, I hope?  The original server uses ffgmx, which
is a different force field.  Also note that the charges assigned by PRODRG are
often unsatisfactory.

> Evertyhting works great know, with the exception of the HG that
> pdb2gmx adds when converting the .pdb into the .gro. This HG is in the
> place that should be taken by the PO3, but I do not know how to remove
> it. Which values will I have to correct in the .top, if any? Should I

Well, if your residue is named SER, the .rtp file used by your force field will
try to assign all the atoms to a standard serine residue.  Then it will add
hydrogen atoms according to the corresponding entry in the .hdb file.

Having never used ffG43a1p, I can't provide a whole lot more input, but I would
also advise against removing parameters from your .top ad hoc.  You need to get
to the source of the problem instead of trying to create a solution.  What went
wrong with ffG43a1p in the first place?  Try searching using the above link, as
I know others have had issues with that particular force field.

-Justin

> just remove the line with all the parameters and just correct the
> subsequent atom numbers? Is there an easier and foolpÅ.oof method to do
> this (it is easy to mistype the numbers this way)?
> Many thanks,
> Nelson
>
> --
> Instituto de Bioquímica Médica
> Universidade Federal do Rio de Janeiro
> Av. Bauhinia 400 CCS, Bl. E, sl 22
> 21941-590
> Ilha do Fundão - Rio de Janeiro - RJ
> Brasil
> Tel: 55-21-2562-6759
> Cel: 55-21-9267-3067
>



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

Justin A. Lemkul
Graduate Research Assistant
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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Message: 5
Date: Thu, 17 Jan 2008 19:39:21 +0100
From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
Subject: Re: [gmx-users] image control
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Message-ID:
	<8ff898150801171039t2003a677u12a12333446c75fb at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi Myunggi Yi,

I said link them, not mail them to me. Check your .tpr file to see 1.
whether these parts of your lipids are already separated at the start of the
equilibration run (you can extract the coordinates with editconf) and 2.
whether you actually have bonds defined where you expect them to be.

Cheers,

Tsjerk

On Jan 16, 2008 3:47 PM, Myunggi Yi <myunggi at gmail.com> wrote:

> I have tried to attach my .gro file, but it is not allowed in mailing
> list.
> I'm attaching small file of the snap shot of the gro file.
> The limit is 50 KB. What can I do?
> I'm attaching the file to you (Tsjerk Wassenaar).
> Again I didn't do any modification.  This is a just output from MD.
> As you know you can check the coordinate in the .gro text file.
> This is not a visulalization problem.
> If any body wants, I will send you my .gro file.
>
> I downloaded popc.itp form Dr. Tieleman's web.
>
> As you see the lipid can be broken any bond (see two fragment of lipid at
> the bottom),
> however the left sile lipid are Okay.
> Any idea?
>
>
> On Jan 16, 2008 7:47 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>
> > Hi Myunggi Yi,
> >
> > In addition, it may help if you give some examples: link the structure
> > file, the topology file, and some sample images highlighting the point your
> > trying to make. Apparently, leaving us guessing doesn't help.
> >
> > Tsjerk
> >
> >
> > On Jan 16, 2008 12:10 AM, Mark Abraham <Mark.Abraham at anu.edu.au > wrote:
> >
> > > Myunggi Yi wrote:
> > > > Thank you.
> > > >
> > > > I know general setup to run a simulation, and I'm running one.
> > > > As you see the title, I have problem with image.
> > >
> > > Well that was a dozen emails ago and we've talked about many topics
> > > since. You'll get nowhere fast by assuming that the people you're
> > > asking
> > > for help have the whole email exchange memorized... they have their
> > > own
> > > problems. To get effective help, describe things fully, and if you
> > > need
> > > to refer back to something, go and get a URL to the mailing list
> > > archives on the GROMACS webpage. This may seem onerous, but you're the
> > > one trying to get free help, so you maximise your chances by making
> > > life
> > > easier on the people who might give it to you.
> > >
> > > > I'm getting broken lipid in the trajectory.
> > >
> > > You're not. mdrun doesn't write broken molecules if they were whole in
> > >
> > > the topology. Your visual representation might have them crossing PBC
> > > boundaries in a way that might make them look broken, however. There
> > > are
> > > many ways to adjust your visual representation, however.
> > >
> > > > Would you let me know how to avoid this?
> > >
> > > As someone else has already suggested, judicious use of trjconv and
> > > the
> > > .gro file you use with VMD are needed here. Read the man page for
> > > trjconv and experiment to find what works for whatever your trying to
> > > do.
> > >
> > > > Do I need special setup?
> > >
> > > No
> > >
> > > Mark
> > > _______________________________________________
> > > gmx-users mailing list     gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please search the archive at http://www.gromacs.org/search before
> > > posting!
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org .
> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > >
> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > Junior UD (post-doc)
> > Biomolecular NMR, Bijvoet Center
> > Utrecht University
> > Padualaan 8
> > 3584 CH Utrecht
> > The Netherlands
> > P: +31-30-2539931
> > F: +31-30-2537623
> >
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> > posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
>
> --
> Best wishes,
>
> MYUNGGI YI
> ==================================
> KLB 419
> Institute of Molecular Biophysics
> Florida State University
> Tallahassee, FL 32306
>
> Office: (850) 645-1334
> http://www.scs.fsu.edu/~myunggi <http://www.scs.fsu.edu/%7Emyunggi>
>
> _______________________________________________
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> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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