<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Oh, I see.</span></div><div><span>I did inserted only the provided values from CHARMM ff prm file. Now I'll do some testing...<br>Thanks Peter,</span></div><div><br><span></span></div><div><font size="1"><i></i></font><font size="1"><i></i></font><div style="font-family:times new roman, new york, times, serif;font-size:14pt;"><style><!--filtered {font-family:"Cambria Math";panose-1:2 4 5 3 5 4 6 3 2 4;}filtered {font-family:Calibri;panose-1:2 15 5 2 2 2 4 3 2 4;}p.MsoNormal, li.MsoNormal, div.MsoNormal {margin-top:0cm;margin-right:0cm;margin-bottom:10.0pt;margin-left:0cm;line-height:115%;font-size:11.0pt;font-family:"sans-serif";}a:link, span.MsoHyperlink {color:blue;text-decoration:underline;}a:visited, span.MsoHyperlinkFollowed {color:purple;text-decoration:underline;}.MsoChpDefault {}.MsoPapDefault
{margin-bottom:10.0pt;line-height:115%;}filtered {margin:70.85pt 3.0cm 70.85pt 3.0cm;}div.Section1 {}--></style><style><!--filtered {font-family:"Cambria Math";panose-1:2 4 5 3 5 4 6 3 2 4;}filtered {font-family:Calibri;panose-1:2 15 5 2 2 2 4 3 2 4;}p.MsoNormal, li.MsoNormal, div.MsoNormal {margin-top:0cm;margin-right:0cm;margin-bottom:10.0pt;margin-left:0cm;line-height:115%;font-size:11.0pt;font-family:"sans-serif";}.MsoChpDefault {}.MsoPapDefault {margin-bottom:10.0pt;line-height:115%;}filtered {margin:70.85pt 3.0cm 70.85pt 3.0cm;}div.Section1 {}--></style><div class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal;"><span style="font-size:8pt;" lang="PT-BR">---</span></div> <div class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal;"><span style="font-size:8pt;" lang="PT-BR"> <font size="1"> </font></span></div><font size="1">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 Paulo.<br>Av.do Café, S/N - ZIP:14040-903 - Ribeirão Preto, São Paulo, Brazil.<br>Phone: +55 16 36024840.</font> <div class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal;"><br><span style="font-size:8pt;" lang="PT-BR"><a rel="nofollow">Curriculum Lattes:</a></span><a rel="nofollow"><span class="texto"> <font size="1">http://lattes.cnpq.br/0777038258459931</font></span></a></div><div class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal;"><span style="font-size:8pt;" lang="PT-BR"><a rel="nofollow">ross_usp@yahoo.com.br</a>,<a rel="nofollow">rsoares@fcfrp.usp.br</a></span></div> <div class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal;"><span style="font-size:8pt;" lang="PT-BR"> </span></div> <br></div></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-family: times new roman, new york, times, serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font size="2" face="Arial"> <hr size="1"> <b><span style="font-weight:bold;">De:</span></b> Peter C. Lai <pcl@uab.edu><br> <b><span style="font-weight: bold;">Para:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org>; gmx gromacs <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Enviadas:</span></b> Sexta-feira, 27 de Abril de 2012 18:39<br> <b><span style="font-weight: bold;">Assunto:</span></b> Re: [gmx-users] gen_pairs to calculate absent 1-4 interactions in CHARMM36c FF<br> </font> </div> <br><div id="yiv1722523098">
<div>btw you only need explicit 1-4 for charmm when the 1,4 from the original charmm prm is actually different/specified (i.e. non-conjugated carbons) <br>
-- <br>
Sent from my Android phone with K-9 Mail. Please excuse my brevity.<br><br><div class="yiv1722523098gmail_quote">"Ricardo O. S. Soares" <ross_usp@yahoo.com.br> wrote:<blockquote class="yiv1722523098gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex;">
<div style="color:#000;background-color:#fff;font-family:times new roman, new york, times, serif;font-size:12pt;"><div><span>Hi Mark,</span></div><div><br><span></span></div><div><span>yeah, I'll try it. <br></span></div><div><br><span></span></div><div><span>Thanks for your reply,</span></div><div><br><span></span></div><div><span>Ricardo.<br></span></div><br><div><br><blockquote style="border-left:2px solid rgb(16, 16, 255);margin-left:5px;margin-top:5px;padding-left:5px;"> <div style="font-family:times new roman, new york, times, serif;font-size:12pt;"> <div style="font-family:times new roman, new york, times, serif;font-size:12pt;"> <div dir="ltr"> <font size="2" face="Arial"> <hr size="1"> <b><span style="font-weight:bold;">De:</span></b> Mark Abraham <Mark.Abraham@anu.edu.au><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, 27 de Abril de 2012 10:43<br> <b><span style="font-weight:bold;">Assunto:</span></b> Re: [gmx-users] gen_pairs to calculate absent 1-4 interactions in CHARMM36c FF<br> </font> </div> <br><div id="yiv1722523098">
<div>
On 27/04/2012 5:21 AM, Ricardo O. S. Soares wrote:
<blockquote type="cite">
<div style="color:#000;background-color:#fff;font-family:times new roman, new york, times, serif;font-size:12pt;">
<div>Dear users,</div>
<div><br>
<span></span></div>
<div>In GROMACS, does CHARMM36 ff, calculate eventual 1-4
interactions that are absent from the [pairtypes] section of
the ffnonbonded.itp file?</div>
<div>I ask this because I'm converting cholesterol parameters
from CHARMM36c to gmx format, and several 1-4 values are
absent in the last two columns of the prm file.</div>
<div>Does setting gen_pairs to "yes" in the [defaults] section
in the forcefield.itp work?<br>
</div>
<br>
</div>
</blockquote>
<br>
Probably. What documentation exists is probably in the walk-through
example of manual 5.7.1. You can probably construct yourself a
trivial test case if you wish to verify how things work.<br>
<br>
Mark<br>
</div>
</div><br>-- <br>gmx-users mailing list <a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a rel="nofollow" target="_blank" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a rel="nofollow" target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists/Search">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" ymailto="mailto:gmx-users-request@gromacs.org" target="_blank" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a rel="nofollow" target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a><br><br> </div>
</div> </blockquote></div> </div></blockquote></div></div></div><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 post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br><br> </div> </div> </blockquote></div> </div></body></html>