[gmx-users] Re: gmx-users Digest, Vol 72, Issue 21

vivek modi modi.vivek2009 at gmail.com
Tue Apr 6 07:16:50 CEST 2010 

On Mon, Apr 5, 2010 at 11:06 PM, <gmx-users-request at gromacs.org> wrote:

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> Today's Topics:
>
>   1. dssp FATAL ERROR. (vivek modi)
>   2. Re: dssp FATAL ERROR. (Justin A. Lemkul)
>   3. Restraints of COM (Eudes Fileti)
>   4. Restraints of COM 2 (Eudes Fileti)
>   5. Topology and force fields (Lum Nforbi)
>   6. Re: Topology and force fields (Gareth Tribello)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 5 Apr 2010 15:42:37 +0530
> From: vivek modi <modi.vivek2009 at gmail.com>
> Subject: [gmx-users] dssp FATAL ERROR.
> To: gmx-users at gromacs.org
> Message-ID:
>        <v2r1d7a8f7a1004050312w1255d51dyb360601b86346dc at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> hi,
>
> Although this is already discussed in the mailing list but none of the
> solutions mentioned helped me.
>
> I am using Gromacs-4.0.5. I downloaded dssp from
> http://swift.cmbi.ru.nl/gv/dssp/HTML/dsspcmbi
> Then I copy this to /usr/local/bin & chmod to executable.
> But when I run the program do_dssp it gives the following error:
>
>
> Program do_dssp_4, VERSION 4.0.5
> Source code file: do_dssp.c, line: 471
>
> Fatal error:
> Failed to execute command: /usr/local/bin/dssp -na ddXnSQTc ddgMjECf >
> /dev/null 2> /dev/null
>
> Any help is appreciated.
>
>
> Thanks.
>
> Vivek Modi,
> Graduate Student, IITK.
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> ------------------------------
>
> Message: 2
> Date: Mon, 05 Apr 2010 06:52:04 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] dssp FATAL ERROR.
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4BB9C0D4.1030207 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> vivek modi wrote:
> > hi,
> >
> > Although this is already discussed in the mailing list but none of the
> > solutions mentioned helped me.
> >
> > I am using Gromacs-4.0.5. I downloaded dssp
> > from http://swift.cmbi.ru.nl/gv/dssp/HTML/dsspcmbi
> > Then I copy this to /usr/local/bin & chmod to executable.
> > But when I run the program do_dssp it gives the following error:
> >
> >
> > Program do_dssp_4, VERSION 4.0.5
> > Source code file: do_dssp.c, line: 471
> >
> > Fatal error:
> > Failed to execute command: /usr/local/bin/dssp -na ddXnSQTc ddgMjECf >
> > /dev/null 2> /dev/null
> >
> > Any help is appreciated.
> >
>
> Did you re-name the executable?  Have you set the DSSP environment variable
> properly?
>
> -Justin
>


Yes. I have done both the things.


Vivek.


>
> >
> > Thanks.
> >
> > Vivek Modi,
> > Graduate Student, IITK.
> >
> >
>
> --
> ========================================
>
> 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
>
> ========================================
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 5 Apr 2010 09:59:23 -0300
> From: Eudes Fileti <fileti at ufabc.edu.br>
> Subject: [gmx-users] Restraints of COM
> To: gmx-users at gromacs.org
> Message-ID:
>        <q2x65e289a21004050559r190f50a9j8eb35736c3839682 at mail.gmail.com>
> Content-Type: text/plain; charset="windows-1252"
>
> Hello everybody, I have two benzene molecules and I
> want to restrain them only by their center of mass. The
> conversation below (between Shirts and Spoel) gave me
> some ideas but still I couldnt solve the problem. In particular
> I'm not seeing any way to create this user group, nor how to
> calculate its center of mass. Could someone give me a
> hand with that?
> Bests
> eef
> _______________________________________
> Eudes Eterno Fileti
> Centro de Ciências Naturais e Humanas
> Universidade Federal do ABC — CCNH
> Av. dos Estados, 5001
> Santo André - SP - Brasil
> CEP 09210-971
> +55.11.4996-0196
> http://fileti.ufabc.edu.br
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> ------------------------------
>
> Message: 4
> Date: Mon, 5 Apr 2010 10:04:20 -0300
> From: Eudes Fileti <fileti at ufabc.edu.br>
> Subject: [gmx-users] Restraints of COM 2
> To: gmx-users at gromacs.org
> Message-ID:
>        <z2t65e289a21004050604t270a616cgfb28c4546e511fb9 at mail.gmail.com>
> Content-Type: text/plain; charset="windows-1252"
>
> Hello everybody, I have two benzene molecules and I want to restrain them
> only by their center of mass. The conversation below (between Shirts and
> Spoel) gave me some ideas but still I couldnt solve the problem. In
> particular I'm not seeing any way to create this user group, nor how to
> calculate its center of mass. Could someone give me a hand with that?
>
> On Sun, 2004-01-25 at 04:00, Michael Shirts wrote:
> > Hello, all-
> >
> > So, supposing I had a protein, and wanted to restrain a ligand by
> attaching
> > it with a spring to some point that wasn't actually an atom -- say it was
> > the center of geometry of a number of atoms around the binding pocket, so
> that
> > it's a point that redefines itself at each step of the simulation.
> >
> > 1) Is this possible to do using either the position restraint or distance
> > restraint tools in GROMACS?
> >
> > 2) If not, how might one modify the code to put this in?
> If this is dynamic, like the centre of mass of a group, you might add
> something using a user group. Compute the center of mass of your user
> group and call the position restraint routine. The good thing (TM) is
> that you don't have to program any I/O.
>
> >
> > Thanks,
> > Michael Shirts
> > Stanford University.
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,   75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org
> http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________
> Eudes Eterno Fileti
> Centro de Ciências Naturais e Humanas
> Universidade Federal do ABC — CCNH
> Av. dos Estados, 5001
> Santo André - SP - Brasil
> CEP 09210-971
> +55.11.4996-0196
> http://fileti.ufabc.edu.br
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> ------------------------------
>
> Message: 5
> Date: Mon, 5 Apr 2010 10:26:53 -0700
> From: Lum Nforbi <lumngwegia at gmail.com>
> Subject: [gmx-users] Topology and force fields
> To: gmx-users at gromacs.org
> Message-ID:
>        <s2rf7e1d8851004051026r675119ffs9ebec4f2e13fc59a at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello all,
>
>        Below are the contents of a water1.top file that I used to simulate
> 2000 molecules of TIP3P water (NPT).  I made this topology file according
> to
> the pattern on page 114 of the manual (topology for Urea in water). My
> diffusion coefficient, viscosity and radial distribution functions matched
> those for tip3p water in literature.
>        Recently I was told that I did not need to use another force field
> in the topology like ffcharmm27.itp since tip3p.itp is already a forcefield
> on its own. Could this be true? I just wanted to verify the authenticity of
> my simulation. If the structure of the topology below is not correct,
> please
> let me know.
>
> ; The force field files to be included
> #include "ffcharmm27.itp"
>
> ; Include TIP3P water topology
> #include "tip3p.itp"
>
> [ system ]
> Pure Water
>
> [ molecules ]
> ;molecule name number
> SOL              1936
> SOL                64
>
> I appreciate your answers.
>
> Lum
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> ------------------------------
>
> Message: 6
> Date: Mon, 5 Apr 2010 19:35:36 +0200
> From: Gareth Tribello <gareth.tribello at gmail.com>
> Subject: Re: [gmx-users] Topology and force fields
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>        <z2xb83620ff1004051035u896a34d4q9cde7833dd0659bc at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello
>
> I think what you have been told is wrong.  You need to include both
> "ffcharmm27.itp" and "tip3p.itp" as the atomtypes in your tip3p.itp will
> otherwise not be defined.  There is an easy way to check though - take out
> the include ffcharmm27.itp and try to run grompp on your new topology.  My
> bet would be that it won't work and, if you are using rigid molecules, it
> will tell you that it finds a settles section in the wrong place.
>
> ciao
> Gareth
>
> On Mon, Apr 5, 2010 at 7:26 PM, Lum Nforbi <lumngwegia at gmail.com> wrote:
>
> > Hello all,
> >
> >         Below are the contents of a water1.top file that I used to
> simulate
> > 2000 molecules of TIP3P water (NPT).  I made this topology file according
> to
> > the pattern on page 114 of the manual (topology for Urea in water). My
> > diffusion coefficient, viscosity and radial distribution functions
> matched
> > those for tip3p water in literature.
> >         Recently I was told that I did not need to use another force
> field
> > in the topology like ffcharmm27.itp since tip3p.itp is already a
> forcefield
> > on its own. Could this be true? I just wanted to verify the authenticity
> of
> > my simulation. If the structure of the topology below is not correct,
> please
> > let me know.
> >
> > ; The force field files to be included
> > #include "ffcharmm27.itp"
> >
> > ; Include TIP3P water topology
> > #include "tip3p.itp"
> >
> > [ system ]
> > Pure Water
> >
> > [ molecules ]
> > ;molecule name number
> > SOL              1936
> > SOL                64
> >
> > I appreciate your answers.
> >
> > Lum
> >
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
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> End of gmx-users Digest, Vol 72, Issue 21
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