Dear Wu, <br>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. <br><br>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.
<br><br>However, to extend the gro file, we need to use the angle information and may be write a script. <br><br>I don't know if this a good idea??<br><br>Mohan <br><br><br><br><div><span class="gmail_quote">On 08/11/06,
<b class="gmail_sendername"><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a></b> <<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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<br><br>Today's Topics:<br><br> 1. Re: Creation of an index file with seperate lipid leaflets<br> (Jay Mashl)<br> 2. Re: pdb2gmx and protein DNA complexes (Erik Marklund)<br> 3. Re: pdb2gmx and protein DNA complexes (Erik Marklund)
<br> 4. How to generate GRO and TOP file for high-number-atom<br> polymer? (WU Yanbin)<br> 5. What if the atom number exceed 99999 for Gromacs file? (WU Yanbin)<br><br><br>----------------------------------------------------------------------
<br><br>Message: 1<br>Date: Wed, 8 Nov 2006 11:32:20 -0600 (CST)<br>From: Jay Mashl <<a href="mailto:mashl@uiuc.edu">mashl@uiuc.edu</a>><br>Subject: Re: [gmx-users] Creation of an index file with seperate lipid<br> leaflets
<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID:<br> <<a href="mailto:Pine.LNX.4.64.0611081107270.29552@kermit.beckman.uiuc.edu">Pine.LNX.4.64.0611081107270.29552@kermit.beckman.uiuc.edu
</a>><br>Content-Type: TEXT/PLAIN; charset=US-ASCII<br><br><br>Wasted work would be bad ;)<br><br>Rather than headgroup orientation, maybe try looking at atom distributions<br>along the bilayer normal direction. Neutron scattering experiments show that
<br>for atom groups far from the bilayer midplane, the corresponding z-coordinates<br>form two distinct distributions. So one way could be the following. Pick a<br>headgroup atom and obtain its z-coordinate. Have make_ndx accept this value as
<br>input. Search the system by looping over lipids and ask whether that atom type<br>has a z-coordinate within some amount around the input value. From this you<br>know the membership of the leaflets. A more automatic way would be to have the
<br>program first discern the distribution and then reread the system to decide the<br>leaflet membership.<br><br>Jay<br><br><br>On Wed, 8 Nov 2006, Alan Dodd wrote:<br>> Wouldn't shuffle/sort undo all the good work? I did
<br>> wonder if I should have labelled the lipids in<br>> different leaflets as different molecule types, or<br>> different chains, but it's a bit late now...<br>><br>> --- Jay Mashl <<a href="mailto:mashl@uiuc.edu">
mashl@uiuc.edu</a>> wrote:<br>><br>> > On Wed, 8 Nov 2006, Alan Dodd wrote:<br>> > > Has anyone already created a way to generate an<br>> > index<br>> > > file with the atoms from the two leaflets of a
<br>> > bilayer<br>> > > listed seperately? I can't believe it hasn't<br>> > already<br>> > > been done, but can't find a direct description of<br>> > a<br>> > > solution. I'm attempting a modification to
<br>> > make_ndx,<br>> > > (or perhaps something considerably less ambitious,<br>> > > judging by the way it's going so far) to permit<br>> > lipid<br>> > > selection based on headgroup orientation, though
<br>> > I'd<br>> > > quite like to save myself the effort.<br>> > > Incidentally, splitres and splitat seem to be the<br>> > > wrong way around, unless I'm misunderstanding them<br>> > -
<br>> > > they do the opposite of what they say. From the<br>> > > gromacs 3.3.1 source download I did on April of<br>> > this<br>> > > year.<br>> ><br>> > Reordering the lipids into leaflets in your starting
<br>> > coordinate<br>> > file might be a good idea. If you anticipate lipid<br>> > exchange between leaflets,<br>> > then a more general tool like what you suggest would<br>> > be helpful.<br>
> ><br>> > Jay<br>> ><br>> > _______________________________________________<br>> > gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> > <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
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gmx-users-request@gromacs.org</a>.<br>> > Can't post? Read<br>> > <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br>> ><br>><br>><br>>
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<br><br>--<br>R. Jay Mashl<br>University of Illinois<br><a href="mailto:mashl@uiuc.edu">mashl@uiuc.edu</a><br>(Tel)217-244-5818<br><br><br>------------------------------<br><br>Message: 2<br>Date: Wed, 8 Nov 2006 18:44:24 +0100
<br>From: "Erik Marklund" <<a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a>><br>Subject: Re: [gmx-users] pdb2gmx and protein DNA complexes<br>To: "Discussion list for GROMACS users" <
<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <004c01c7035d$87aea500$ccc5f382@mimer><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>Yes, very recently actually. What forcefield are you using? If you're using the AMBERXX-port, you might want to have a look at
<a href="http://folding.stanford.edu/ffamber/">http://folding.stanford.edu/ffamber/</a>. 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.<br><br>
/Erik<br> ----- Original Message -----<br> From: Debojyoti Dutta<br> To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br> Sent: Wednesday, November 08, 2006 6:08 PM<br> Subject: [gmx-users] pdb2gmx and protein DNA complexes
<br><br><br> Hi<br><br> 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.<br><br> Program pdb2gmx, VERSION 3.3<br> Source code file: resall.c
, line: 438<br><br> Fatal error:<br> Residue 'C' not found in residue topology database<br><br> The pdb segment is as follows:<br><br> ATOM 1239 NZ LYS B 513 -24.159 16.372 -25.774 1.00 51.42 N<br>
ATOM 1249 N1 C C 1 - 10.253 8.018 40.704 1.00 25.86 N<br><br> Has anyone encountered this problem before?<br><br> Regards<br> Debo<br><br> --<br> ---------------------------------------------
<br> Debojyoti Dutta, PhD (USC)<br> <a href="http://catarina.usc.edu/~ddutta">http://catarina.usc.edu/~ddutta</a><br> ---------------------------------------------<br><br><br><br>------------------------------------------------------------------------------
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<br><br>Message: 3<br>Date: Wed, 8 Nov 2006 18:49:49 +0100<br>From: "Erik Marklund" <<a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a>><br>Subject: Re: [gmx-users] pdb2gmx and protein DNA complexes
<br>To: "Discussion list for GROMACS users" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <006b01c7035e$493ad4f0$ccc5f382@mimer><br>Content-Type: text/plain; charset="iso-8859-1"
<br><br>...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.<br><br>/Erik<br> ----- Original Message -----
<br> From: Erik Marklund<br> To: Discussion list for GROMACS users<br> Sent: Wednesday, November 08, 2006 6:44 PM<br> Subject: Re: [gmx-users] pdb2gmx and protein DNA complexes<br><br><br> Yes, very recently actually. What forcefield are you using? If you're using the AMBERXX-port, you might want to have a look at
<a href="http://folding.stanford.edu/ffamber/">http://folding.stanford.edu/ffamber/</a>. 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.<br><br>
/Erik<br> ----- Original Message -----<br> From: Debojyoti Dutta<br> To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br> Sent: Wednesday, November 08, 2006 6:08 PM<br> Subject: [gmx-users] pdb2gmx and protein DNA complexes
<br><br><br> Hi<br><br> 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.<br><br> Program pdb2gmx, VERSION 3.3<br> Source code file:
resall.c, line: 438<br><br> Fatal error:<br> Residue 'C' not found in residue topology database<br><br> The pdb segment is as follows:<br><br> ATOM 1239 NZ LYS B 513 -24.159 16.372 -25.774 1.00 51.42
N<br> ATOM 1249 N1 C C 1 - 10.253 8.018 40.704 1.00 25.86 N<br><br> Has anyone encountered this problem before?<br><br> Regards<br> Debo<br><br> --<br> ---------------------------------------------
<br> Debojyoti Dutta, PhD (USC)<br> <a href="http://catarina.usc.edu/~ddutta">http://catarina.usc.edu/~ddutta</a><br> ---------------------------------------------<br><br><br><br>----------------------------------------------------------------------------
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<br><br>Message: 4<br>Date: Wed, 8 Nov 2006 16:32:11 -0600<br>From: "WU Yanbin" <<a href="mailto:ywu27@uiuc.edu">ywu27@uiuc.edu</a>><br>Subject: [gmx-users] How to generate GRO and TOP file for<br> high-number-atom polymer?
<br>To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Message-ID:<br> <<a href="mailto:3b43155a0611081432n12d444b9qf78896237d1f9b65@mail.gmail.com">3b43155a0611081432n12d444b9qf78896237d1f9b65@mail.gmail.com
</a>><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>Hi,<br> Genearlly I generate GRO and TOP file for polymer using PRODRG. But<br>PRODRG does not work when the atom number of the polymer exceeds 300. So can
<br>anyone recommend other software and method? Thanks.<br><br>Yours Sincerely,<br><br>WU Yanbin<br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <a href="http://www.gromacs.org/pipermail/gmx-users/attachments/20061108/7b74d68f/attachment-0001.html">
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<a href="mailto:ywu27@uiuc.edu">ywu27@uiuc.edu</a>><br>Subject: [gmx-users] What if the atom number exceed 99999 for Gromacs<br> file?<br>To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Message-ID:
<br> <<a href="mailto:3b43155a0611081611u223052efid4ed718e5acfc62@mail.gmail.com">3b43155a0611081611u223052efid4ed718e5acfc62@mail.gmail.com</a>><br>Content-Type: text/plain; charset="iso-8859-1"<br>
<br>Hi,<br> I built up a box of polymer with box size 20x20x20 and then solvate the<br>box with water using Genbox. Thus the total atom number exceeds 99999 and I<br>found that the atom number starts from zero when it exceeds 99999. Does it
<br>matter for the ongoing command "grompp" and "mdrun"? Thanks.<br><br>Yours Sincerely,<br><br>WU Yanbin<br><br>--<br>-----------------------------------------------------------------------------------------------------------------------
<br>WU Yanbin<br>Department of Mechanical Science and Engineering Email:<br><a href="mailto:ywu27@uiuc.edu">ywu27@uiuc.edu</a><br>3323 Beckman Institute<br>Phone: (217)819-9064<br>University of Illinois at Urbana-Champaign
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