[gmx-users] Re: How to generate GRO and TOP file for
Mohan Boggara
mohanbabu.boggara at gmail.com
Sat Nov 11 21:34:29 CET 2006
Dear Wu,
I had exactly the same question to ask the users. I hope someone would give
a better idea to generate gro and itp for a polymer of your choice molecular
weight.
Currently, what I am doing is to create a smaller polymer using prodrg and
manually extend the itp to the size I want. I know this is not the best way,
however, since polymer topology has just same pattern, its easy to create
the itp file.
However, to extend the gro file, we need to use the angle information and
may be write a script.
I don't know if this a good idea??
Mohan
On 08/11/06, gmx-users-request at gromacs.org <gmx-users-request at gromacs.org>
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> Today's Topics:
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> 1. Re: Creation of an index file with seperate lipid leaflets
> (Jay Mashl)
> 2. Re: pdb2gmx and protein DNA complexes (Erik Marklund)
> 3. Re: pdb2gmx and protein DNA complexes (Erik Marklund)
> 4. How to generate GRO and TOP file for high-number-atom
> polymer? (WU Yanbin)
> 5. What if the atom number exceed 99999 for Gromacs file? (WU Yanbin)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 8 Nov 2006 11:32:20 -0600 (CST)
> From: Jay Mashl <mashl at uiuc.edu>
> Subject: Re: [gmx-users] Creation of an index file with seperate lipid
> leaflets
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <Pine.LNX.4.64.0611081107270.29552 at kermit.beckman.uiuc.edu>
> Content-Type: TEXT/PLAIN; charset=US-ASCII
>
>
> Wasted work would be bad ;)
>
> Rather than headgroup orientation, maybe try looking at atom distributions
> along the bilayer normal direction. Neutron scattering experiments show
> that
> for atom groups far from the bilayer midplane, the corresponding
> z-coordinates
> form two distinct distributions. So one way could be the following. Pick
> a
> headgroup atom and obtain its z-coordinate. Have make_ndx accept this
> value as
> input. Search the system by looping over lipids and ask whether that atom
> type
> has a z-coordinate within some amount around the input value. From this
> you
> know the membership of the leaflets. A more automatic way would be to
> have the
> program first discern the distribution and then reread the system to
> decide the
> leaflet membership.
>
> Jay
>
>
> On Wed, 8 Nov 2006, Alan Dodd wrote:
> > Wouldn't shuffle/sort undo all the good work? I did
> > wonder if I should have labelled the lipids in
> > different leaflets as different molecule types, or
> > different chains, but it's a bit late now...
> >
> > --- Jay Mashl <mashl at uiuc.edu> wrote:
> >
> > > On Wed, 8 Nov 2006, Alan Dodd wrote:
> > > > Has anyone already created a way to generate an
> > > index
> > > > file with the atoms from the two leaflets of a
> > > bilayer
> > > > listed seperately? I can't believe it hasn't
> > > already
> > > > been done, but can't find a direct description of
> > > a
> > > > solution. I'm attempting a modification to
> > > make_ndx,
> > > > (or perhaps something considerably less ambitious,
> > > > judging by the way it's going so far) to permit
> > > lipid
> > > > selection based on headgroup orientation, though
> > > I'd
> > > > quite like to save myself the effort.
> > > > Incidentally, splitres and splitat seem to be the
> > > > wrong way around, unless I'm misunderstanding them
> > > -
> > > > they do the opposite of what they say. From the
> > > > gromacs 3.3.1 source download I did on April of
> > > this
> > > > year.
> > >
> > > Reordering the lipids into leaflets in your starting
> > > coordinate
> > > file might be a good idea. If you anticipate lipid
> > > exchange between leaflets,
> > > then a more general tool like what you suggest would
> > > be helpful.
> > >
> > > Jay
> > >
> > > _______________________________________________
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> >
> >
> >
> >
> >
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>
> --
> R. Jay Mashl
> University of Illinois
> mashl at uiuc.edu
> (Tel)217-244-5818
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 8 Nov 2006 18:44:24 +0100
> From: "Erik Marklund" <erikm at xray.bmc.uu.se>
> Subject: Re: [gmx-users] pdb2gmx and protein DNA complexes
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID: <004c01c7035d$87aea500$ccc5f382 at mimer>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Yes, very recently actually. What forcefield are you using? If you're
> using the AMBERXX-port, you might want to have a look at
> http://folding.stanford.edu/ffamber/. Regardless of your ff, make sure
> that the atoms in your pdb match the ones in ff[your_forcefield].rtp. Oh,
> and read the manual.
>
> /Erik
> ----- Original Message -----
> From: Debojyoti Dutta
> To: gmx-users at gromacs.org
> Sent: Wednesday, November 08, 2006 6:08 PM
> Subject: [gmx-users] pdb2gmx and protein DNA complexes
>
>
> Hi
>
> I am trying to simulate a protein DNA complex but I am stuck at the
> pdb2gmx stage as it gets stuck when it encounters a nucleotide.
>
> Program pdb2gmx, VERSION 3.3
> Source code file: resall.c, line: 438
>
> Fatal error:
> Residue 'C' not found in residue topology database
>
> The pdb segment is as follows:
>
> ATOM 1239 NZ LYS B 513 -24.159 16.372 -25.774 1.00 51.42
> N
> ATOM 1249 N1 C C 1 - 10.253 8.018 40.704 1.00 25.86
> N
>
> Has anyone encountered this problem before?
>
> Regards
> Debo
>
> --
> ---------------------------------------------
> Debojyoti Dutta, PhD (USC)
> http://catarina.usc.edu/~ddutta
> ---------------------------------------------
>
>
>
>
> ------------------------------------------------------------------------------
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> Message: 3
> Date: Wed, 8 Nov 2006 18:49:49 +0100
> From: "Erik Marklund" <erikm at xray.bmc.uu.se>
> Subject: Re: [gmx-users] pdb2gmx and protein DNA complexes
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID: <006b01c7035e$493ad4f0$ccc5f382 at mimer>
> Content-Type: text/plain; charset="iso-8859-1"
>
> ...and not just the atoms. Make sure that the residue names are the
> correct ones for your forcefield. Apparently, the forcefield you're using
> does not have a 'C'-residue.
>
> /Erik
> ----- Original Message -----
> From: Erik Marklund
> To: Discussion list for GROMACS users
> Sent: Wednesday, November 08, 2006 6:44 PM
> Subject: Re: [gmx-users] pdb2gmx and protein DNA complexes
>
>
> Yes, very recently actually. What forcefield are you using? If you're
> using the AMBERXX-port, you might want to have a look at
> http://folding.stanford.edu/ffamber/. Regardless of your ff, make sure
> that the atoms in your pdb match the ones in ff[your_forcefield].rtp. Oh,
> and read the manual.
>
> /Erik
> ----- Original Message -----
> From: Debojyoti Dutta
> To: gmx-users at gromacs.org
> Sent: Wednesday, November 08, 2006 6:08 PM
> Subject: [gmx-users] pdb2gmx and protein DNA complexes
>
>
> Hi
>
> I am trying to simulate a protein DNA complex but I am stuck at the
> pdb2gmx stage as it gets stuck when it encounters a nucleotide.
>
> Program pdb2gmx, VERSION 3.3
> Source code file: resall.c, line: 438
>
> Fatal error:
> Residue 'C' not found in residue topology database
>
> The pdb segment is as follows:
>
> ATOM 1239 NZ LYS B 513 -24.159 16.372 -25.774 1.00 51.42
> N
> ATOM 1249 N1 C C 1 - 10.253 8.018 40.704 1.00 25.86
> N
>
> Has anyone encountered this problem before?
>
> Regards
> Debo
>
> --
> ---------------------------------------------
> Debojyoti Dutta, PhD (USC)
> http://catarina.usc.edu/~ddutta
> ---------------------------------------------
>
>
>
>
> ----------------------------------------------------------------------------
>
>
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> ------------------------------
>
> Message: 4
> Date: Wed, 8 Nov 2006 16:32:11 -0600
> From: "WU Yanbin" <ywu27 at uiuc.edu>
> Subject: [gmx-users] How to generate GRO and TOP file for
> high-number-atom polymer?
> To: gmx-users at gromacs.org
> Message-ID:
> <3b43155a0611081432n12d444b9qf78896237d1f9b65 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
> Genearlly I generate GRO and TOP file for polymer using PRODRG. But
> PRODRG does not work when the atom number of the polymer exceeds 300. So
> can
> anyone recommend other software and method? Thanks.
>
> Yours Sincerely,
>
> WU Yanbin
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> ------------------------------
>
> Message: 5
> Date: Wed, 8 Nov 2006 18:11:42 -0600
> From: "WU Yanbin" <ywu27 at uiuc.edu>
> Subject: [gmx-users] What if the atom number exceed 99999 for Gromacs
> file?
> To: gmx-users at gromacs.org
> Message-ID:
> <3b43155a0611081611u223052efid4ed718e5acfc62 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
> I built up a box of polymer with box size 20x20x20 and then solvate
> the
> box with water using Genbox. Thus the total atom number exceeds 99999 and
> I
> found that the atom number starts from zero when it exceeds 99999. Does it
> matter for the ongoing command "grompp" and "mdrun"? Thanks.
>
> Yours Sincerely,
>
> WU Yanbin
>
> --
>
> -----------------------------------------------------------------------------------------------------------------------
> WU Yanbin
> Department of Mechanical Science and Engineering Email:
> ywu27 at uiuc.edu
> 3323 Beckman Institute
> Phone: (217)819-9064
> University of Illinois at Urbana-Champaign
> 405 N. Mathews Avenue
> Urbana, IL 61801
>
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--
Mohan Boggara
Graduate Research Assistant
Dept of Chemical Engineering
University of Houston
S222 Engg Bldg 1, 4800 Calhoun Rd,
Houston, Texas-77204, USA
Mobile: 1-832-643-5729
Office: 1-713-743-4314
http://polymer.chee.uh.edu/
Strive for excellence and not for perfection --Kamal Hassan, Indian Actor
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