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<div>Or just do it by hand and replace the lines in the .top with each protein chains .itp file.</div>
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<div>Stephan</div>
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<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Freitag, 17. Mai 2013 um 16:17 Uhr<br/>
<b>Von:</b> "Mark Abraham" <mark.j.abraham@gmail.com><br/>
<b>An:</b> "Discussion list for GROMACS users" <gmx-users@gromacs.org><br/>
<b>Betreff:</b> Re: [gmx-users] Expanding a .top file to have all connection information</div>
<div name="quoted-content">How does grompp -pp look?<br/>
<br/>
Mark<br/>
<br/>
<br/>
On Fri, May 17, 2013 at 3:40 PM, davidjrosenman <davidjrosenman@gmail.com>wrote:<br/>
<br/>
> Hello everyone,<br/>
><br/>
> This may be a bit out of the purview of this list, but it can't hurt to<br/>
> ask.<br/>
><br/>
> Let me start from the beginning: I'm trying to take a structure/topology<br/>
> that I generated with GROMACS tools and convert it to run with NAMD. The<br/>
> problem is that this is a huge simulation box with many different atom<br/>
> types<br/>
> (homodimeric protein, water, lipids, ions), and I am having a lot of<br/>
> trouble<br/>
> generating a .psf file from the information I have.<br/>
><br/>
> The current strategy I'm pursuing to accomplish this task is to use the<br/>
> top2psf script:<br/>
> <a href="http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/top2psf/" target="_blank">http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/top2psf/</a><br/>
><br/>
> The issue is that this script will only read what is explicitly written in<br/>
> the top file. All of the include records will be ignored, as will multiple<br/>
> molecules. So, the output is a psf suitable ONLY for the first chain of my<br/>
> dimer. I want a psf that will include all components of my structure,<br/>
> including the lipids, waters, etc.<br/>
><br/>
> So, I ask, is there a way to expand a topology to explicitly get all of the<br/>
> connectivities in a structure? I figure this information must be contained<br/>
> in the .tpr file, but that's neither human readable nor compatible with<br/>
> top2psf.<br/>
><br/>
> If you have any advice for that, or for the larger problem at hand, I would<br/>
> appreciate it. Thank you very much!<br/>
><br/>
> Cheers,<br/>
> David Rosenman<br/>
> Grad Student, Rensselaer Polytechnic Institute<br/>
><br/>
><br/>
><br/>
><br/>
> --<br/>
> View this message in context:<br/>
> <a href="http://gromacs.5086.x6.nabble.com/Expanding-a-top-file-to-have-all-connection-information-tp5008345.html" target="_blank">http://gromacs.5086.x6.nabble.com/Expanding-a-top-file-to-have-all-connection-information-tp5008345.html</a><br/>
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.<br/>
> --<br/>
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