I see. Well, maybe doing the old school manual carving isn't a bad idea, after all. I still think your script is extremely useful, will definitely write to you if I need it.<div><br></div><div>Thanks,</div><div><br></div>
<div>Alex</div><div><br><br><div class="gmail_quote">On Thu, May 6, 2010 at 1:44 AM, Kukol, Andreas <span dir="ltr"><<a href="mailto:a.kukol@herts.ac.uk">a.kukol@herts.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Alex,<br>
<br>
I used the membrane builder and even developed a script to convert that POPC into Gro53a6 - please contact me by personal email, if you want it.<br>
<br>
Afterwards I found, that the resulting protein/lipid system contained many overlaps between atoms and removing all the overlaps created a membrane with many holes. So in conclusion using the membrane builder was a waste of time.<br>
<font color="#888888"><br>
Andreas<br>
</font><div class="im"><br>
<br>
> -----Original Message-----<br>
> From: <a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>]<br>
> On Behalf Of Alex Smolyanitsky<br>
> Sent: 06 May 2010 04:58<br>
> To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> Subject: [gmx-users] Lipid topologies, carving, etc<br>
><br>
> Hi everyone,<br>
><br>
> I am setting up an ion channel in a lipid, and in the past<br>
> I would manually carve the membrane using something like PyMol.<br>
><br>
> This time tried the very nice automatic system builder at<br>
> <a href="http://www.charmm-gui.org/?doc=input/membrane" target="_blank">http://www.charmm-gui.org/?doc=input/membrane</a> and the result is<br>
> beautiful. However, the POPC isn't compatible with what's out there<br>
> for the GROMACS 53a6 forcefield, and DPPC isn't compatible with the<br>
> existing rtp entry in 53a6 (a bunch of wrong atom types).<br>
><br>
> Other than doing it manually, is there a quick way to make any of<br>
> the resulting lipid coordinates compatible with GROMACS?<br>
><br>
</div><div><div></div><div class="h5">> Also, is there any software other than the inflategro script and<br>
> g_membed that helps automate the protein-lipid assembly?<br>
><br>
> Thanks a bunch,<br>
><br>
> Alex<br>
><br>
><br>
> --<br>
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</div></div></blockquote></div><br></div>