ied with DESMOND On Fri, May 25, 2012 at 10:38 PM, <[email protected]> wrote:
> Send gmx-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > 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 <[email protected]> > Subject: Re: [gmx-users] Re: One molculetype for 3 proteins > To: Discussion list for GROMACS users <[email protected]> > Message-ID: > <cabze1sjq-7g5vy+zjca4g6pbmnbw2y8eag4zg4ebzlhqcso...@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" <[email protected]> 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 <[email protected] > >wrote: > > > > > > > > On Thu, May 24, 2012 at 10:04 PM, Francesca < > > [email protected]> 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... > > > > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120525/026e0e93/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Fri, 25 May 2012 09:47:38 -0700 (PDT) > From: Francesca <[email protected]> > Subject: [gmx-users] Re: One molculetype for 3 proteins > To: [email protected] > Message-ID: <[email protected]> > 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" <[email protected]> > Subject: [gmx-users] Re: FCC lattice of argon > To: ahmed sta <[email protected]> > Cc: [email protected] > Message-ID: > <capxdd+zqyukclqs1yquq7ea3skzmmsyc-tgsxf4oqgctbcw...@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 <[email protected]> wrote: > > Can you help me please > > > > > > Thanks for all > > > > ________________________________ > > De : Dr. Vitaly V. Chaban <[email protected]> > > À : ahmed sta <[email protected]> > > Cc : [email protected] > > 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 <[email protected]> > 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 <[email protected]> > >> À : ahmed sta <[email protected]> > >> Cc : [email protected] > >> 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 <[email protected]> > 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 <[email protected]> > >>> À : ahmed sta <[email protected]> > >>> Cc : [email protected] > >>> 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 <[email protected]> > >>> 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 <[email protected]> > >>>> À : ahmed sta <[email protected]> > >>>> Cc : [email protected] > >>>> 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 <[email protected]> > >>>> 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 > >>>>> [email protected] > >>>> > >>>> > >>> > >>> > >> > >> > > > > > > > > -- > > 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" <[email protected]> > Subject: Re: [gmx-users] ptn ptn interaction > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > 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" <[email protected]> > Subject: Re: [gmx-users] Simulation protocol for Protein-DNA-complex > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > 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 > > ======================================== > > > ------------------------------ > > -- > gmx-users mailing list > [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > 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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