<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div><span>All right. <br></span></div><div><span>Thank you so much.</span></div><div><span>Shima</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" size="2"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br> <b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Sunday, May 6, 2012 11:32 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Topology parameters<br> </font> </div> <br>
<br><br>On 5/6/12 2:36 PM, Shima Arasteh wrote:<br>> IS the parameters for a residue in CHARMM36 and CHARMM27 the same?<br>><br><br>I would suggest you do a bit of reading about the CHARMM force field hierarchy <br>and why they are named as they are. If you're parameterizing a new residue you <br>can do it for either, or both, depending on the parameter set. In your case, <br>I'd suspect your formyl parameters are going to be universal between CHARMM27 <br>and CHARMM36, but don't let my suggestion be your justification. If a reviewer <br>asks, "some guy on the Internet said it" is not sufficient justification ;)<br><br>-Justin<br><br>> Thanks in advance,<br>> Shima<br>><br>> --------------------------------------------------------------------------------<br>> *From:* Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>> *To:* Discussion list for
GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> *Sent:* Saturday, May 5, 2012 9:16 PM<br>> *Subject:* Re: [gmx-users] Topology parameters<br>><br>><br>><br>> On 5/5/12 11:39 AM, Shima Arasteh wrote:<br>> > Can I use CHARMM-GUI to get the formyl parameters for CHARMM36 and CHARMM27?<br>> ><br>><br>> Maybe, try it and see. Swiss-Param might also be an option.<br>><br>> -Justin<br>><br>> -- ========================================<br>><br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]<a target="_blank" href="http://vt.edu">vt.edu</a> <http://vt.edu> | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>><br>>
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http://www.gromacs.org/Support/Mailing_Lists<br>><br>><br><br>-- <br>========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>-- <br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">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 href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before
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