<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><br></div><div><br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; margin-top: 5px; padding-left: 5px;"> <div style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; "> <div style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; "> <div dir="ltr"> <font size="2" face="Arial"> <hr size="1"> <b><span style="font-weight:bold;">De:</span></b> David van der Spoel <spoel@xray.bmc.uu.se><br> <b><span style="font-weight: bold;">Para:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Enviadas:</span></b> Sexta-feira, 23 de Março de 2012 14:31<br> <b><span style="font-weight: bold;">Assunto:</span></b> Re: [gmx-users] Charmm Cholesterol parameters - str to itp<br> </font> </div>
<br>On 2012-03-23 15:31, Ricardo O. S. Soares wrote:<br>> Hi GMX-users,<br>><br>> Klauda et al (J. Phys. Chem. B, 2012, 116(1), pp 203–210) recently<br>> provided Cholesterol parameters for Charmm FF.<br>> Does anyone know/have a protocol or script to convert the .str file to a<br>> valid .itp file for Charmm within GROMACS?<br>> I understand that Dr. Spoel and colleagues (*J. Am. Chem. Soc.*, 2012,<br>> DOI: 10.1021/ja211929h) are providing cholesterol .itp for OPLS-AA.<br>> Could that maybe be a different starting point?<br>><br>> Thanks for eventual reply,<br><br>Here's a script that has been used for this purpose. Please use with <br>care and *check your output*.<br><br><br></div><div style="font-family: times new roman, new york, times, serif; font-size: 12pt;" class="yui_3_2_0_17_133252354140074"><br></div><div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"
class="yui_3_2_0_17_133252354140074">Thank you David, that is really helpful! </div><div style="font-family: times new roman, new york, times, serif; font-size: 12pt;" class="yui_3_2_0_17_133252354140074">I'll give it a try!</div><div style="font-family: times new roman, new york, times, serif; font-size: 12pt;" class="yui_3_2_0_17_133252354140074">Cheers<br><br><br><br><br>><br>> Ricardo.<br>><br>> ////<br>><br>> ---<br>> Ricardo O. S. Soares , PhD Student.<br>> Group of Biological Physics - Department of Physics & Chemistry<br>> Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São<br>> Paulo.<br>> Av.do Café, S/N - ZIP:14040-903 - Ribeirão Preto, São Paulo, Brazil.<br>> Phone: +55 16 36024840.<br>><br>> .<br>> .<br>><br>><br>><br><br><br>-- <br>David van der Spoel, Ph.D., Professor of Biology<br>Dept. of Cell & Molec. Biol., Uppsala University.<br>Box 596,
75124 Uppsala, Sweden. Phone: +46184714205.<br><a ymailto="mailto:spoel@xray.bmc.uu.se" href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><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 posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't
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