Will I write two .rtp files for two different molecules ? or Will I write one rtp file that includes all parameters of these two molecules ? And how can I use the rtp file when creating the input files ( .gro and .top ) ?
Thanks in advance --- On Thu, 3/12/09, Justin A. Lemkul <jalem...@vt.edu> wrote: From: Justin A. Lemkul <jalem...@vt.edu> Subject: Re: [gmx-users] pdb files To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Date: Thursday, March 12, 2009, 12:11 PM oguz gurbulak wrote: > Dear Justin, > > Can I get a itp file tempate for OPLS-AA according to your suggestions below > and editing the itp file for my molecule. Is it possible to do this ? Or is > there an alternative way apart from manually writing the itp file for OPLS-AA > ? > You're stuck either writing an .rtp entry for use with pdb2gmx, or writing the .itp yourself. -Justin > Thanks in advance > > > > <<You will not want to create a topology from these files, because pdb2gmx > would create a huge mess of files to deal with (a different topology for each > chain). What you want is to do is to create .itp files for each individual > molecule type in your system. This will probably have to be done by hand if > you want to use OPLS-AA. Depending on the complexity of your molecule, you > may be able to use an .rtp entry, but I would suggest processing a single > molecule of this type with pdb2gmx to create a .top for that molecule (which > can be converted to a .itp for later use).<< > > > > --- On *Sat, 3/7/09, Justin A. Lemkul /<jalem...@vt.edu>/* wrote: > > > From: Justin A. Lemkul <jalem...@vt.edu> > Subject: Re: [gmx-users] pdb files > To: gurbulako...@yahoo.com, "Discussion list for GROMACS users" > <gmx-users@gromacs.org> > Date: Saturday, March 7, 2009, 9:28 AM > > > > oguz gurbulak wrote: > > > Dear All, > > > > > I want to use packmol pdb files that includes one or two > different types of molecules. And I seached Gromacs manuals, > tutorials and mail archives in order to have enough information > about using packmol pdb files in Gromacs. But I couldn't find any > information. So Could you please give me the information about this > ? How can I use a packmol pdb file for oplsaa and gromacs > united-atom force field in generating .gro and .top files for md > simulations? > > > > > You will not want to create a topology from these files, because > pdb2gmx would create a huge mess of files to deal with (a different > topology for each chain). What you want is to do is to create .itp > files for each individual molecule type in your system. This will > probably have to be done by hand if you want to use OPLS-AA. >Depending on the complexity of your molecule, you may be able to use > an .rtp entry, but I would suggest processing a single molecule of > this type with pdb2gmx to create a .top for that molecule (which can > be converted to a .itp for later use). > > Do not use the "Gromacs force field" (ffgmx); it is deprecated and > should not be used for new simulations. Use a newer Gromos96 > variant. You can get Gromos96-compatible topologies from the PRODRG > 2.5 server, but be warned that the charges and charge groups > assigned by PRODRG are often inconsistent and unsatisfactory, > requiring manual alteration and validation. > > Summary: > 1. Create .itp files for each molecule type individually. > 2. Construct a .top yourself, which would be as simple as: > > #include "ffoplsaa.itp" > > #include "molecule_A.itp" > #include "molecule_B.itp" > > #include "spc.itp" > #include "ions.itp" > > [ system ] > packmol system > > [ molecules ] > Molecule_A N > Molecule_B N > SOL N > (then whatever ions you need, if any) > > -Justin > > > > > Sincerely > > > > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > </mc/compose?to=gmx-us...@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-requ...@gromacs.org > </mc/compose?to=gmx-users-requ...@gromacs.org>. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- ======================================== > > Justin A. Lemkul > Graduate Research Assistant > ICTAS Doctoral Scholar > 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://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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ======================================== Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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