<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"><div style="color: black; font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; ">Okay, so I am able to create cnt.rtp, and cnt.top file using g_x2top. But g_x2top only supports OPLSAA, and GROMOS forcefield, and if I use a different forcefield then I get this error: Fatal Error: No or incorrect atomname2type.n2t file found,</div><div><font class="Apple-style-span" face="'times new roman', 'new york', times, serif" size="3">which is </font><font class="Apple-style-span" face="'times new roman', 'new york', times, serif">because</font><font class="Apple-style-span" face="'times new roman', 'new york', times, serif" size="3"> other forcefields don't contain any .n2t files. And, I don't want to create cnt.top using oplsaa/gromos because these forcefields are not
suitable for dna. So what is the way around i.e if I can't use the same force field to construct both (cnt and dna) topologies, then what do I do? </font></div><div style="color: black; font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><br></div><div style="color: black; font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; ">Is any of following likely to work (though I don't think so):</div><div style="color: black; font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><br></div><div style="color: black; font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; ">1) Create cnt.top and cnt.rtp using x2top oplsaa, and add cnt.rtp in amber?</div><div style="color: black; font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; ">2) Add an atomname2type.n2t in amber?</div><div style="color: black; font-family: 'times new roman', 'new york', times,
serif; font-size: 12pt; "><br></div><div><font class="Apple-style-span" face="'times new roman', 'new york', times, serif" size="3">Lastly, the link </font><a href="http://cs86.com/CNSE/SWNT.htm" style="color: black; font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; ">http://cs86.com/CNSE/SWNT.htm</a><font class="Apple-style-span" face="'times new roman', 'new york', times, serif" size="3"> doesn't contain anything at the moment. Has it been replaced by some other link or is it </font><font class="Apple-style-span" face="'times new roman', 'new york', times, serif">permanently</font><font class="Apple-style-span" face="'times new roman', 'new york', times, serif" size="3"> down? </font></div><div><font class="Apple-style-span" face="'times new roman', 'new york', times, serif" size="3"><br></font></div><div><font class="Apple-style-span" face="'times new roman', 'new york', times, serif"
size="3">Thanks,</font></div><div><font class="Apple-style-span" face="'times new roman', 'new york', times, serif" size="3">Majid</font></div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; color: black; "><br><div style="font-family:arial, helvetica, sans-serif;font-size:10pt"><font size="2" face="Tahoma"><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> Mon, April 18, 2011 10:25:39 AM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Simulation of CNT with Amber forcefield<br></font><br>
<br><br>majid hasan wrote:<br>> Dear All,<br>> <br>> I am doing a DNA-CNT simulation, and I am trying to generate a topology of CNT using Amber99, which has been used for such systems, and CNT atoms are modeled using sp2 carbon parameters.<br>> <br>> But when I try to create topology file using: pdb2gmx -f cnt.pdb -p cnt.top, and Amber99 forcefield, I get this error:<br><br>Have you created an .rtp entry for your CNT? I doubt that it's even possible for cyclic molecules like this one. pdb2gmx is only useful for linear molecules composed of repeating building blocks, with limited support for branching. You may want to consult:<br><br><span><a target="_blank" href="http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube">http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube</a></span><br><br>Some of that information is outdated, but there is a plethora of information in the list archive about proper CNT topology
generation. Search for posts by Christopher Stiles.<br><br>> Fatal Error: Atom C in residue C 1 was not found in rtp entry RCN with 30 atoms while sorting atoms.<br>> <br><br>This answers my question above. Your structure is being interpreted as RNA. Without significant effort and perhaps code modification, pdb2gmx is not likely to be useful here.<br><br>> During the execution, it says "There are 1 chains and 0 blocks of water and 1 residues with 168 atoms" after analyzing pdb file.<br>> <br>> So I suspect problem is that it reads carbon as a residue in my .pdb file. <br>> If this is the problem, then how do I make sure that it reads carbon as an atom and not a residue?<br>> <br>> My .pdb file has entries of the form:<br>> ATOM 1 C C A 1 4.039 ....<br>> ATOM 2 C C A 1 3.97 ....<br>>
<br><br>Well, you've named your residues "C" and the component atoms "C" so there's no real confusion about anything. It's also not the source of your problems.<br><br>g_x2top may be a useful program for generating a topology, or perhaps other software that is entirely unrelated to Gromacs.<br><br>-Justin<br><br>> Thanks for your help,<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 ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br><span>Can't post? Read <a target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a></span><br></div></div><div style="position: fixed; color: black; font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "></div>
</div></body></html>