<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt">Just a little addition to my previous reply: if I run the same procedure with oplsaa, it works. Now in Oplsaa, I added following two lines in already existing .n2t lines,<br> CA opls_239 0 12.011 3 C 0.142 C 0.142 C 0.142<br> CA opls_239 0 12.011 2 C 0.142 C 0.142<br> <br>But oplsaa also has a bunch of other atoms named opls... , but I guess these don't matter because nanotube only has Carbon bonded with 1,2, or 3, atoms, so I only added three lines for these carbons in amber99.n2t<br><br>Thanks,<br>Majid<br><div><br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><div
style="font-family: arial,helvetica,sans-serif; font-size: 10pt;"><font face="Tahoma" 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> Tue, April 19, 2011 10:40:53 AM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] atomname2type.n2t file for CNT in amber99<br></font><br>
<br><br>majid hasan wrote:<br>> Dear All,<br>> <br>> In an attempt to create CNT topology with g_x2top and amber99, I was getting this error: no or incorrect atomname2type.n2t file found. So I tried to create a atomname2type.n2t file for CNT in Amber99. My coordinate file is of this form:<br>> UNNAMED<br>> 400<br>> 1TUB CA 1 0.392 0.000 0.000<br>> so I opened oplsaa's .n2t file, and replaced all the entries with these three lines:<br>> CA C 0 12.011 3 C 0.142 C 0.142 C 0.142<br>> CA CA 0 12.011 2 C 0.142 C 0.142<br>> CA CB 0 12.011 1 C 0.142 <br>> C, CA, CB are all listed in
atomtypes.atp file in Amber as:<br>> C 12.01000 ; sp2 C carbonyl group<br>> CA 12.01000 ; sp2 C pure aromatic (benzene)<br>> CB 12.01000 ; sp2 aromatic C, 5&6 membered ring junction<br>> <br>> <br>> But when I run the g_x2top, I still get the same error.<br>> <br><br>And where is this .n2t file located? It needs to be in the amber99.ff directory to actually work, and you need to provide this force field's name in your g_x2top command, which unfortunately you have not posted.<br><br>-Justin<br><br>> Any help is much appreciated.<br>> <br>> Thanks,<br>> Majid<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]<a target="_blank" href="http://vt.edu">vt.edu</a> | (540) 231-9080<br><span><a target="_blank" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a></span><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><span><a target="_blank" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a></span><br><span>Please search the archive at <a target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!</span><br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a
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