<br><br><div class="gmail_quote">On Sat, May 12, 2012 at 9:49 AM, Shima Arasteh <span dir="ltr"><<a href="mailto:shima_arasteh2001@yahoo.com" target="_blank">shima_arasteh2001@yahoo.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><div style="font-size:12pt;font-family:arial,helvetica,sans-serif"><div><span>Dear gmx users,</span></div><div><br><span></span></div><div><span>Anybody can guide me to some articles which introduces CHARMM36 forcefield? I want to study about this forcefield.</span></div>
<div><br></div></div></div></blockquote><div><br>Have a look at this paper:<br><br><a href="http://pubs.acs.org/doi/abs/10.1021/jp101759q">http://pubs.acs.org/doi/abs/10.1021/jp101759q</a><br><br> -Anirban<br><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><div style="font-size:12pt;font-family:arial,helvetica,sans-serif"><div><span></span></div><div><span>Thanks in advance,</span></div><div><span>Shima<br></span></div><div><br></div> <div style="font-family:arial,helvetica,sans-serif;font-size:12pt">
<div style="font-family:times new roman,new york,times,serif;font-size:12pt"> <div dir="ltr"> <font face="Arial"><div class="im"> <hr size="1"> <b><span style="font-weight:bold">From:</span></b> Anirban <<a href="mailto:reach.anirban.ghosh@gmail.com" target="_blank">reach.anirban.ghosh@gmail.com</a>><br>
<b><span style="font-weight:bold">To:</span></b> Shima Arasteh <<a href="mailto:shima_arasteh2001@yahoo.com" target="_blank">shima_arasteh2001@yahoo.com</a>>; Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>> <br>
</div><b><span style="font-weight:bold">Sent:</span></b> Friday, May 11, 2012 9:22 PM<div><div class="h5"><br> <b><span style="font-weight:bold">Subject:</span></b> Re: [gmx-users] Simulation of POPC in water using CHARMM27<br>
</div></div></font> </div><div><div class="h5"> <br>
<div><br><br>
<div>On Fri, May 11, 2012 at 10:08 PM, Shima Arasteh <span dir="ltr"><<a rel="nofollow" href="mailto:shima_arasteh2001@yahoo.com" target="_blank">shima_arasteh2001@yahoo.com</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex">
<div>
<div style="FONT-FAMILY:arial,helvetica,sans-serif;FONT-SIZE:14pt">
<div><font size="3"><span>CHARMM27 or CHARMM36 doesn't make different for me. I just want to get a good output of simulation.</span></font></div>
<div><font size="3"><span>Before this, Justin also suggested me for CHARMM36. Ok, I will use CHARMM36. But about the atom types, it's not still clear for me what I need to do. If I use the CHARMM36, am I supposed to build berger lipids?</span></font></div>
<div><font size="3"><span><br></span></font></div></div></div></blockquote>
<div> </div>
<div>Actually if you use CHARMM36 FF then no need to use Berger parameters, since CHARMM36 FF already have the all-atom POPC parameters. But there are differences among the atom types. So you can use these POPC files (Peter Lai provided me these files and these were generated for the following work: (please reference):<br>
Lai, P.C. and Crasto, C.J.<br>Beyond Modeling: All-Atom Olfactory Receptor Model Simulations<br>Front. Gene.<br>Volume 3 Year 2012 Number 61<br>DOI: 10.3389/fgene.2012.00061) </div>
<div> </div>
<div>These files worked fine for me (with grompp). Include the popc.itp file in your .top file.</div>
<div> </div>
<div>-Anirban</div>
<div> </div>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex">
<div>
<div style="FONT-FAMILY:arial,helvetica,sans-serif;FONT-SIZE:14pt">
<div><font size="3"><span>Thanks,</span></font></div>
<div><span><font size="3">Shima</font><br></span></div>
<div><br></div>
<div style="FONT-FAMILY:arial,helvetica,sans-serif;FONT-SIZE:14pt">
<div style="FONT-FAMILY:times new roman,new york,times,serif;FONT-SIZE:12pt">
<div dir="ltr"><font face="Arial">
<div>
<hr size="1">
<b><span style="FONT-WEIGHT:bold">From:</span></b> Anirban <<a rel="nofollow" href="mailto:reach.anirban.ghosh@gmail.com" target="_blank">reach.anirban.ghosh@gmail.com</a>><br><b><span style="FONT-WEIGHT:bold">To:</span></b> Shima Arasteh <<a rel="nofollow" href="mailto:shima_arasteh2001@yahoo.com" target="_blank">shima_arasteh2001@yahoo.com</a>> <br>
</div><b><span style="FONT-WEIGHT:bold">Sent:</span></b> Friday, May 11, 2012 8:58 PM
<div>
<div><br><b><span style="FONT-WEIGHT:bold">Subject:</span></b> Re: [gmx-users] Simulation of POPC in water using CHARMM27<br></div></div></font></div>
<div>
<div><br>
<div><br><br>
<div>On Fri, May 11, 2012 at 9:13 PM, Shima Arasteh <span dir="ltr"><<a rel="nofollow" href="mailto:shima_arasteh2001@yahoo.com" target="_blank">shima_arasteh2001@yahoo.com</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex">
<div>
<div style="FONT-FAMILY:arial,helvetica,sans-serif;FONT-SIZE:14pt">
<div><span>Dear Anirban,</span></div>
<div><span>No, I have not done. Because I didn't know I need Berger lipids for this simulation. <br></span></div></div></div></blockquote>
<div> </div>
<div>Actually I think the coordinate and topology files from Tieleman's site are in accordance with the Berger lipid parameters and hence works with the united-atom gromos FF. You can also get CHARMM27 lipids from <a href="http://terpconnect.umd.edu/%7Ejbklauda/research/download.html" target="_blank">http://terpconnect.umd.edu/~jbklauda/research/download.html</a> here. And the atom-type errors can be solved if you can build a proper .hdb file with the proper corrections for the violating atom names.</div>
<div> </div>
<div>-Anirban</div>
<div> </div>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex">
<div>
<div style="FONT-FAMILY:arial,helvetica,sans-serif;FONT-SIZE:14pt">
<div><span>Thanks for you reply,</span></div>
<div><span>Cheers,</span></div>
<div><span>Shima<br></span></div>
<div>
<div><br></div></div>
<div style="FONT-FAMILY:arial,helvetica,sans-serif;FONT-SIZE:14pt">
<div></div>
<div style="FONT-FAMILY:times new roman,new york,times,serif;FONT-SIZE:12pt">
<div>
<div dir="ltr"><font face="Arial">
<hr size="1">
<b><span style="FONT-WEIGHT:bold">From:</span></b> Anirban <<a rel="nofollow" href="mailto:reach.anirban.ghosh@gmail.com" target="_blank">reach.anirban.ghosh@gmail.com</a>><br><b><span style="FONT-WEIGHT:bold">To:</span></b> Shima Arasteh <<a rel="nofollow" href="mailto:shima_arasteh2001@yahoo.com" target="_blank">shima_arasteh2001@yahoo.com</a>>; Discussion list for GROMACS users <<a rel="nofollow" href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>> <br>
<b><span style="FONT-WEIGHT:bold">Sent:</span></b> Friday, May 11, 2012 8:10 PM<br><b><span style="FONT-WEIGHT:bold">Subject:</span></b> Re: [gmx-users] Simulation of POPC in water using CHARMM27<br></font></div></div>
<div>
<div><br>
<div><br><br>
<div>On Fri, May 11, 2012 at 7:36 PM, Shima Arasteh <span dir="ltr"><<a rel="nofollow" href="mailto:shima_arasteh2001@yahoo.com" target="_blank">shima_arasteh2001@yahoo.com</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex">
<div>
<div style="FONT-FAMILY:arial,helvetica,sans-serif;FONT-SIZE:24pt">
<div><font size="4">Dear gmx users,</font></div>
<div><font size="4"><br></font></div>
<div><font size="4">I'm going to simulate the POPC in water.</font></div>
<div><font size="4">I downloaded required files in Tielman site and made the .top file. Then included the CHARMM27.ff in the .top file.</font></div>
<div><font size="4">When I run the grompp I get the fatal error as below:</font></div>
<div><font size="4">Atomtype CB not found<br></font></div>
<div><font size="4"><br></font></div>
<div><font size="4">I have done the same with gromos87.ff . But I didn't see any error.</font></div>
<div><font size="4">What's the problem?</font></div>
<div><font size="4">Anybody may suggest me how to solve this problem? Is this because of the forcefield? Or something in .top file goes wrong?</font></div>
<div><font size="4"><br></font></div></div></div></blockquote>
<div><br>Have properly edited the CHARMM27 bonded and nonbonded .itp files to include the Berger lipid parameters and have you included the POPC topology? You can follow this tutorial to get an idea:<br><br><a rel="nofollow" href="https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial" target="_blank">https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial</a><br>
<br>-Anirban<br> </div>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex">
<div>
<div style="FONT-FAMILY:arial,helvetica,sans-serif;FONT-SIZE:24pt">
<div><font size="4"></font></div>
<div><font size="4">Thanks,</font></div>
<div><font size="4">Shima</font><br></div></div></div><br>--<br>gmx-users mailing list <a rel="nofollow" href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a rel="nofollow" href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a rel="nofollow" href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</blockquote></div><br></div><br><br></div></div></div></div></div></div></blockquote></div><br></div><br><br></div></div></div></div></div></div></blockquote></div><br>
</div><br><br> </div></div></div> </div> </div></div></blockquote></div><br>