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<div class=Section1><pre><font size=2 face="Courier New"><span
style='font-size:10.0pt'>>>Christopher Stiles wrote:<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><i><span
style='font-style:italic'> RE: gmx-users Digest, Vol 39, Issue 25, 4<o:p></o:p></span></i></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><i><span
style='font-style:italic'> <o:p></o:p></span></i></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><i><span
style='font-style:italic'> It wasn't apparent to me that it was so simple, I copied the ffgmx.n2t file<o:p></o:p></span></i></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><i><span
style='font-style:italic'> from the GMXLIB to my working dir and renamed it to ffG43b1.n2t and it<o:p></o:p></span></i></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><i><span
style='font-style:italic'> worked just fine with x2top. One catch though<o:p></o:p></span></i></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><i><span
style='font-style:italic'> <o:p></o:p></span></i></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><i><span
style='font-style:italic'> When I use x2top with the following command:<o:p></o:p></span></i></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><i><span
style='font-style:italic'> <o:p></o:p></span></i></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><i><span
style='font-style:italic'> x2top -f testH.pdb -o testH.top -r testH.rtp<o:p></o:p></span></i></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><i><span
style='font-style:italic'> <o:p></o:p></span></i></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><i><span
style='font-style:italic'> it does not create the testH.rtp file, but does properly make the testH.top<o:p></o:p></span></i></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><i><span
style='font-style:italic'> file.<o:p></o:p></span></i></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><i><span
style='font-style:italic'> <o:p></o:p></span></i></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><i><span
style='font-style:italic'> So my question is there a trick or does it go some where else or maybe it<o:p></o:p></span></i></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><i><span
style='font-style:italic'> just will not do it for my SWCNT<o:p></o:p></span></i></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><i><span
style='font-style:italic'> <o:p></o:p></span></i></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><i><span
style='font-style:italic'> Also I have searched the archives and found this problem popped up many<o:p></o:p></span></i></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>><i><span
style='font-style:italic'> other times bit no solution is given that I can locate.<o:p></o:p></span></i></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>you can try either -r or -o but you don't need the rtp anyway. note that <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>you can use the pbc flag to get an infinite CNT.<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>-- <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>David van der Spoel, Ph.D.<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>Molec. Biophys. group, Dept. of Cell & Molec. Biol., <st1:place
w:st="on"><st1:PlaceName w:st="on">Uppsala</st1:PlaceName> <st1:PlaceType
w:st="on">University</st1:PlaceType></st1:place>.<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>>Box 596, 75124 <st1:place
w:st="on"><st1:City w:st="on">Uppsala</st1:City>, <st1:country-region w:st="on">Sweden</st1:country-region></st1:place>. Phone: +46184714205. Fax: +4618511755.<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>><a
href="http://www.gromacs.org/mailman/listinfo/gmx-users">spoel at xray.bmc.uu.se</a> <a
href="http://www.gromacs.org/mailman/listinfo/gmx-users">spoel at gromacs.org</a> <a
href="http://folding.bmc.uu.se">http://folding.bmc.uu.se</a><o:p></o:p></span></font></pre>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I am not 100% sure how I should respond to these (as in
format) but let me know if there is a preferred method.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Ok what I am trying to do is use the *.top and the *.rtp
file with pdb2gmx to make my *.gro file to use with editconf and genbox ect…
I take it there is a better/easier way to do this?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<pre><font size=2 face="Courier New"><span style='font-size:10.0pt'>Thank you very much for your help!<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>~Christopher Stiles <o:p></o:p></span></font></pre><pre><st1:place
w:st="on"><st1:PlaceType w:st="on"><font size=2 face="Courier New"><span
style='font-size:10.0pt'>College</span></font></st1:PlaceType> of <st1:PlaceName
w:st="on">Nanoscale</st1:PlaceName></st1:place> Science and Engineering (CNSE)<o:p></o:p></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>State <st1:PlaceType
w:st="on">University</st1:PlaceType> of <st1:PlaceName w:st="on">New York</st1:PlaceName>, <st1:place
w:st="on"><st1:City w:st="on">Albany</st1:City>, <st1:State w:st="on">New York</st1:State> <st1:PostalCode
w:st="on">12203</st1:PostalCode>, <st1:country-region w:st="on">USA</st1:country-region></st1:place><o:p></o:p></span></font></pre>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
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