[gmx-users] Re: gmx-users Digest, Vol 97, Issue 196
rethina malliga
sgrm.bu at gmail.com
Sat May 26 13:51:40 CEST 2012
ied with DESMOND
On Fri, May 25, 2012 at 10:38 PM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
>
> 1. Re: Re: One molculetype for 3 proteins (Tsjerk Wassenaar)
> 2. Re: One molculetype for 3 proteins (Francesca)
> 3. Re: FCC lattice of argon (Dr. Vitaly V. Chaban)
> 4. Re: ptn ptn interaction (Justin A. Lemkul)
> 5. Re: Simulation protocol for Protein-DNA-complex (Justin A. Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 25 May 2012 15:47:20 +0200
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> Subject: Re: [gmx-users] Re: One molculetype for 3 proteins
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <CABzE1SjQ-7g5vY+Zjca4G6pbmNbw2y8eaG4zG4eBzLhqCsONLg at mail.gmail.com
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Steven,
>
> There will be three dihedrals spanning a break. Make sure to remove all of
> them. Of course pdb2gmx shouldn't just connect the chain ends... Maybe you
> can file it as a bug.
>
> Cheers,
>
> Tsjerk
>
> On May 25, 2012 3:11 PM, "Steven Neumann" <s.neumann08 at gmail.com> wrote:
>
> Yes, it works (-chainsep interactive: merge = yes ) but when you process to
> grompp there is an error:
>
> Unknown cmap torsion between atoms 6002 6004 6006 6017 6021
>
> pdb2gmx takes the cmap for the atoms e.g. last two residues of chain A with
> first three residues of chain B. Removing these lines does not solve the
> problem. Any suggestions appreciated!
>
>
>
> On Fri, May 25, 2012 at 9:57 AM, Steven Neumann <s.neumann08 at gmail.com
> >wrote:
>
> >
> >
> > > On Thu, May 24, 2012 at 10:04 PM, Francesca <
> > francesca.stanzione at unina.it> wrote: >> >> I checked ...
> >
> > Yes, it works (-chainsep interactive: merge = no ) but when you process
> to
> > grompp there is an error:
> >
> > Unknown cmap torsion between atoms 6002 6004 6006 6017 6021
> >
> > pdb2gmx takes the cmap for the atoms e.g. last two residues of chain A
> > with first three residues of chain B. Does removing this lines will be
> > reasonable or some torsions wont be taken into account?
> >
> > Steven
> >
> > >> >> >> -- >> View this message in context:
> > http://gromacs.5086.n6.nabble.com/One-molculetype-for-3...
> >
> >
>
> --
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> ------------------------------
>
> Message: 2
> Date: Fri, 25 May 2012 09:47:38 -0700 (PDT)
> From: Francesca <francesca.stanzione at unina.it>
> Subject: [gmx-users] Re: One molculetype for 3 proteins
> To: gmx-users at gromacs.org
> Message-ID: <1337964458119-4997773.post at n6.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
> if you create a bond you need to have angle, tortion etc...
> Maybe when you processed pb2gmx it create a bond between the 799 and 801.
> Francesca
>
> --
> View this message in context:
> http://gromacs.5086.n6.nabble.com/One-molculetype-for-3-proteins-tp4997727p4997773.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 25 May 2012 12:56:08 -0400
> From: "Dr. Vitaly V. Chaban" <vvchaban at gmail.com>
> Subject: [gmx-users] Re: FCC lattice of argon
> To: ahmed sta <ahmedsta6600 at yahoo.fr>
> Cc: gmx-users at gromacs.org
> Message-ID:
> <CAPXdD+ZQyUkcLqs1YquQ7eA3SkZMMSYC-TgsXF4oQgctBcW1Mw at mail.gmail.com
> >
> Content-Type: text/plain; charset=ISO-8859-1
>
> Ahmed -
>
> This is *YOUR* research, not mine. I believe I have given you enough
> hints to succeed.
>
>
> Dr. Vitaly V. Chaban, 430 Hutchison Hall
> Dept. Chemistry, University of Rochester
> 120 Trustee Road, Rochester, NY 14627-0216
> THE UNITED STATES OF AMERICA
>
>
>
> On Fri, May 25, 2012 at 12:51 PM, ahmed sta <ahmedsta6600 at yahoo.fr> wrote:
> > Can you help me please
> >
> >
> > Thanks for all
> >
> > ________________________________
> > De : Dr. Vitaly V. Chaban <vvchaban at gmail.com>
> > À : ahmed sta <ahmedsta6600 at yahoo.fr>
> > Cc : gmx-users at gromacs.org
> > Envoyé le : Vendredi 25 mai 2012 17h33
> > Objet : Re: Re : Re : Re : Gromacs
> >
> > Sure, possible.
> >
> > But if you want to type the coordinates for FCC lattice using 500
> > atoms by hand, that's indeed cool.
> >
> >
> >
> > On Fri, May 25, 2012 at 11:31 AM, ahmed sta <ahmedsta6600 at yahoo.fr>
> wrote:
> >> I thought that it is possible to use text editor in order to fix the
> >> geometry, isn't it?
> >>
> >>
> >> ________________________________
> >> De : Dr. Vitaly V. Chaban <vvchaban at gmail.com>
> >> À : ahmed sta <ahmedsta6600 at yahoo.fr>
> >> Cc : gmx-users at gromacs.org
> >> Envoyé le : Vendredi 25 mai 2012 18h15
> >> Objet : Re: Re : Re : Gromacs
> >>
> >> Writing your program has nothing to do with gromacs. If you do not
> >> have experience in programming by far, it may be faster to use the
> >> second route. But of you still want to generate a program yourself, I
> >> am delighted to direct your attention to the PYTHON, python.org,
> >> programming language.
> >>
> >> I am aware of some commercial software like MedeA and (perhaps?)
> >> Materials Studio, capable to generate molecular configurations of
> >> various symmetries. Maybe, someone in the gromacs mailing list can
> >> suggest a free alternative as well.
> >>
> >>
> >>
> >> On Fri, May 25, 2012 at 11:05 AM, ahmed sta <ahmedsta6600 at yahoo.fr>
> wrote:
> >>> Well i see
> >>>
> >>> I think that writing my own program would be better and more accurate
> >>> How should i proceed ?
> >>> it is my first use of Gromacs and i do not know how to do
> >>>
> >>> Regards
> >>>
> >>> ________________________________
> >>> De : Dr. Vitaly V. Chaban <vvchaban at gmail.com>
> >>> À : ahmed sta <ahmedsta6600 at yahoo.fr>
> >>> Cc : gmx-users at gromacs.org
> >>> Envoyé le : Vendredi 25 mai 2012 17h58
> >>> Objet : Re: Re : Gromacs
> >>>
> >>> If you want a solid system, where atoms are arranged as in FCC, this
> >>> is another talk.
> >>>
> >>> There two way to achieve your goal. Either --
> >>>
> >>> 1) you write a simple program which places argon atoms as in FCC.
> >>>
> >>> OR
> >>>
> >>> 2) you try to freeze my system into your system using simulated
> >>> annealing implemented in gromacs. Provided that argon is a pretty
> >>> simple system, this should not take too much time. At least, I can say
> >>> that our students get it (216 atoms) freezed during one laboratory
> >>> work.
> >>>
> >>> BTW, there is no guarantee that the freezing point of the classical
> >>> argon model is perfectly reproduced. My guess is based on the fact
> >>> that the density of the liquid phase (in the NPT ensemble) is not
> >>> ideal.
> >>>
> >>>
> >>> Dr. Vitaly V. Chaban, 430 Hutchison Hall
> >>> Dept. Chemistry, University of Rochester
> >>> 120 Trustee Road, Rochester, NY 14627-0216
> >>> THE UNITED STATES OF AMERICA
> >>>
> >>>
> >>>
> >>> On Fri, May 25, 2012 at 10:44 AM, ahmed sta <ahmedsta6600 at yahoo.fr>
> >>> wrote:
> >>>> Sorry. My aim is to model FCC Argon (not liquid state) and i am trying
> >>>> to
> >>>> define that geometry
> >>>> Can you help me please?
> >>>>
> >>>> Regards
> >>>>
> >>>> ________________________________
> >>>> De : Dr. Vitaly V. Chaban <vvchaban at gmail.com>
> >>>> À : ahmed sta <ahmedsta6600 at yahoo.fr>
> >>>> Cc : gmx-users at gromacs.org
> >>>> Envoyé le : Vendredi 25 mai 2012 17h36
> >>>> Objet : Re: Gromacs
> >>>>
> >>>> Dear Ahmed -
> >>>>
> >>>> I do not understand how you imagine "FCC geometry" in the liquid state
> >>>> of matter.
> >>>>
> >>>> If you want to just resize my system, use the standard "genbox"
> >>>> utility and then re-equilibrate at the desired temperature and density
> >>>> (if you want to fix density, of course).
> >>>>
> >>>>
> >>>> Dr. Vitaly V. Chaban, 430 Hutchison Hall
> >>>> Dept. Chemistry, University of Rochester
> >>>> 120 Trustee Road, Rochester, NY 14627-0216
> >>>> THE UNITED STATES OF AMERICA
> >>>>
> >>>>
> >>>>
> >>>> On Fri, May 25, 2012 at 10:30 AM, ahmed sta <ahmedsta6600 at yahoo.fr>
> >>>> wrote:
> >>>>> Dear Vitaly
> >>>>>
> >>>>>
> >>>>> I am an engineer student and i am now trying to use Gromacs
> >>>>> I found your Argon molecule defined topology created in May 2009
> >>>>> I want to ask you how to define my own geometry on Gromacs
> >>>>> In fact i am trying to define liquid Argon system with a density
> >>>>> equilibrated at 90K. My system should have a FCC geometry and
> >>>>> containing
> >>>>> for
> >>>>> example 500 atoms
> >>>>>
> >>>>>
> >>>>> I really need your help
> >>>>>
> >>>>> Best regards
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> Ahmed Sta
> >>>>> Ensta Paristech engineering school
> >>>>> ahmedsta6600 at yahoo.fr
> >>>>
> >>>>
> >>>
> >>>
> >>
> >>
> >
> >
> >
> > --
> > Dr. Vitaly V. Chaban, 430 Hutchison Hall
> > Dept. Chemistry, University of Rochester
> > 120 Trustee Road, Rochester, NY 14627-0216
> > THE UNITED STATES OF AMERICA
> >
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 25 May 2012 09:30:45 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] ptn ptn interaction
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4FBF8985.6040200 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 5/25/12 3:19 AM, rethina malliga wrote:
>
> > On 5/24/12 7:43 AM, rethina malliga wrote:
> > > Hi,
> > >
> > > I tried protein protein simulation in gromacs.
> > >
> > > I prepared one ptn and kept seperately with its .top, .itp, .gro
> files.
> > >
> > > Then I prepared another protein and I build the complex of
> pasting the
> > .gro file
> > > of first processed protein in the .gro file of second processed
> ptn.
> > >
> > > In the topol.top of second protein I included the molecule type
> at the
> > bottom
> > > and inserted
> > > ;Include ligand topology
> > > #include "posre.itp"
> > >
> >
> > Be careful about name clashes here - the first protein (by default)
> will have a
> > file named "posre.itp" that will be applied to it. If you use the
> same name for
> > different files, you'll probably get other errors. I find it useful
> to call
> > everything based on specific names, like "posre_proteinA.itp" or
> something
> > similar.
> >
> > > And i run succeccfully the newbox generation, solvent adding
> commands.
> > >
> > > But with the ions adding command it shows fatal error that the
> atoms in
> > > topol.top and solv.gro is different.
> > >
> > > `Fatal error:
> > > number of coordinates in coordinate file (solv.gro, 231262)
> > > does not match topology (topol.top, 237548)
> > >
> > > on analysing the difference between two files i come to know that
> it is
> > taking
> > > the atoms of first protein for the second protein though i named
> first and
> > > second proteins different.
> > >
> >
> > After you added the second protein, did you correctly update the
> [molecules]
> > section of the topology?
> >
> > > I changed the residue information in .gro of first file to 1LIG
> and change
> > > everything regarding second molecules name as 1LIG
> > >
> >
> > Unless your protein residues are all called LIG, then this is not
> appropriate.
> >
> > > and after retrying the ions adding command it says no such
> molecule type
> > found.
> > >
> > > `Fatal error:
> > > No such moleculetype 1LIG
> > > For more information and tips for troubleshooting, please check
> the GROMACS
> > > website at http://www.gromacs.org/Documentation/Errors
> > >
> >
> > This comes from incorrect naming. Updating [molecules] correctly
> with the name
> > of your second protein [moleculetype] will solve it. Make sure you
> make changes
> > to both the coordinate file and topology at all steps - they should
> always
> > match.
>
> > Hi Justin,
> >
> > I tried again with correct namings. If I leave the original name for
> second
> > protein molecule type (Protein_chain_A) unaltered it shows difference
> in atoms
> > of topol.top and solv.gro. If I alter the molecule type, where ever its
> instance
> > appears it shows molecule type not found.
> >
> > Thanks in advance
> >
>
> Please don't reply to the entire digest message; it becomes hopelessly
> confusing. Your approach of leaving the original names in place is the
> best way
> to proceed. As for the error that arises about coordinates and topology
> not
> matching, consult this document:
>
>
> http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
>
> The solution is always better bookkeeping. You may wish to start over,
> prior to
> solvation, and have tools like genbox and genion do all the bookkeeping
> for you
> by invoking the -p flag with each.
>
> >Justin,
>
>Hi,
>>Sorry for the inconvenience.
>Thank you for your reply and will u please advice me protein protein
simulation tutorial for gromacs.
>
> ------------------------------
>
> Message: 5
> Date: Fri, 25 May 2012 11:32:12 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Simulation protocol for Protein-DNA-complex
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4FBFA5FC.30803 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-15; format=flowed
>
>
>
> On 5/25/12 10:01 AM, Matthias Ernst wrote:
> > Hi,
> >
> > I have a question regarding simulation of a protein-DNA-complex where the
> > protein encloses the DNA double helix. I did not find a tutorial for a
> system of
> > three rather big molecules like these, that's why I ask. If there is
> such, I
> > would appreciate a hint.
> >
>
> In principle, it is no different from the lysozyme tutorial cited below.
> The
> workflow starts with pdb2gmx, which can handle all the molecules in the
> system
> (protein and water) and then you solvate, add ions, and simulate. There's
> not
> much very special in this case.
>
> > I want to start with a crystal structure from PDB. When I do the steps
> in J.
> > Lemkuls tutorial "Lysozyme in water", first thing would be an energy
> > minimization in vacuo. Unfortunately, doing this I end up with the two
> strands
> > of the DNA double helix being far away from the protein and seperated
> from each
> > other. Can this result from clashes and therefore high energy in the
> system that
> > allows the DNA strands to move "through" the protein or how else can this
> > happen? And how can I prevent this?
> >
>
> I suspect this is more a result of periodicity than anything else.
> Depending on
> how bad the initial geometry is, this in vacuo minimization may not be
> completely necessary. You can test an in vacuo minimization by using "pbc
> = no"
> and/or setting an unreasonably large box with:
>
> editconf -f conf.gro -o hugebox.gro -c -d 10
>
> In this instance, with the protein/DNA complex centered in a huge box,
> there's
> no way you'll get breaks across periodic boundaries during EM.
>
> > I mean, usually the protocol is:
> > - minimize system in vacuo
> > - add solvent and ions
> > - minimize again
> > - add thermostat and barostat
> > - simulate
> > Obviously, I cannot follow this if the first step already does not work.
> When I
> > tried to skip in-vacuo-minimization and to minimize the system in
> solvent, it
> > ended up bei either reaching machine precision without the maximum force
> being
> > small enough or in the simulation, the atom were moving to fast. Would
> it be a
> > good idea to use position restraints for the minimizations? If yes, for
> which
> > part, in which order and in which steps?
> >
>
> Position restraints for EM will likely make the outcome worse, as any
> necessary
> tweaks that may need to happen during EM will be disfavored due to the
> applied
> restraints. I never use position restraints during EM for similar systems.
> Perhaps one can think of instances where some restraints might be useful,
> but I
> don't think this is one of them.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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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>
> End of gmx-users Digest, Vol 97, Issue 196
> ******************************************
>
--
Regards,
Rethina.
Rethina Malliga Gunasekaran,
Department Of BioInformatics,
Science Block,
Alagappa University,
Karaikudi – 630 003, India.
http://alagappauniversity.academia.edu/RethinamalligaGunasekaran/
**
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