<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>Yes, of course. But right now I am just trying to make sure that my input files are all correct, and then I will dig into these actual forcefields.</div><div><br></div><div>Thanks a lot,</div><div>Majid</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 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> Gromacs Users' List <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Fri, April 8, 2011 3:14:47 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] .n2t file for ssDNA<br></font><br>
<br><br>majid hasan wrote:<br>> Okay, I'll try to create a better .pdb file, and see how it goes. So if oplsaa doesn't have nucleic acids, then Amber is a better choice?<br>> <br><br>A force field should be chosen based on thorough study of the literature, including the derivation of the parameter sets and their inherent assumptions and limitations, as well as their success in reproducing relevant physical observables. This is the most important choice you likely make when starting a simulation, so you shouldn't simply choose a force field because it's there and might "work" in terms of getting some form of output.<br><br>-Justin<br><br>> Thanks,<br>> Majid<br>> <br>> ------------------------------------------------------------------------<br>> *From:* Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>> *To:* Gromacs Users' List <<a
ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> *Sent:* Fri, April 8, 2011 3:03:23 PM<br>> *Subject:* Re: [gmx-users] .n2t file for ssDNA<br>> <br>> <br>> <br>> majid hasan wrote:<br>> > Thanks Justin!<br>> > But with pdb2gmx, after selecting force field and water model, I get this error: Fatal Error: Residue 'DA3' not found in residue topology (on selecting oplsaa), and when I selected amber99, I got following fatal<br>> <br>> Right, there are no nucleic acids in OPLS-AA by default. There may be parameters out there somewhere, but they're not in Gromacs.<br>> <br>> > error: there is a dangling bond at at least one of the terminal ends and the force field doesn't provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file.<br>> ><br>> <br>> This is not a broadly-applicable error message,
unfortunately, contrary to what it might suggest. Nucleic acid termini do not use .n.tdb or .c.tdb files; these are for proteins. Regardless, your input file has to conform to the requirements of the .rtp entries for the force field. You're probably missing atoms.<br>> <br>> > I also tried Amber, and Oplsaa forcefields on a different dna.pdb file, and got missing residue errors.<br>> <br>> Then the input is not sound and thus is not a good test case.<br>> <br>> -Justin<br>> <br>> > Any help would be much appreciated.<br>> ><br>> > Thanks,<br>> > Majid<br>> ><br>> > ------------------------------------------------------------------------<br>> > *From:* Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> <mailto:<a ymailto="mailto:jalemkul@vt.edu"
href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>>><br>> > *To:* Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>>><br>> > *Sent:* Fri, April 8, 2011 12:54:38 PM<br>> > *Subject:* Re: [gmx-users] .n2t file for ssDNA<br>> ><br>> ><br>> ><br>> > majid hasan wrote:<br>> > > Dear All,<br>> > ><br>> > > I am trying to simulate the interaction between DNA, and CNT. But when I try to create the toplogy file with command<br>> > ><br>> > > g_x2top -f ssdna.gro -o ssdna.top -ff select, I get the following error: Fatal error: Could only find a forcefield type for
119 out of 287 atoms<br>> > ><br>> > > I am using the oplsaa forcefield, and I suspect it is because atomname2type.n2t file doesn't contain all the possible bonds in it. Copy of my .n2t file is attached with the message. Could you please guide me how to add all these<br>> > > possible bonds in my .n2t file?<br>> > ><br>> ><br>> > That would be a very time-consuming exercise, and likely (certainly) g_x2top is not the best tool for this job, for several reasons, the most obvious being that a number of force fields (AMBER and CHARMM, at least) have native support for nucleic acids via pdb2gmx.<br>> ><br>> > g_x2top can certainly create a topology for a CNT, but it requires basically one line, since the geometry is all the same. Then just #include your cnt.itp file in your system topology and you're
done.<br>> ><br>> > -Justin<br>> ><br>> > > I also downloaded the ffoplsaanr, ffoplsaano, from user contributed gromacs forcefields, but these packages also don't have .n2t file.<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><span> <<a target="_blank" href="http://vt.edu">http://vt.edu</a>> <</span><a href="http://vt.edu" target="_blank">http://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> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<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>>> Please search the archive at <br><span>> <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> <mailto:<a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>> <mailto:<a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> <mailto:<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>> <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]vt.edu | (540) 231-9080<br>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</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> <mailto:<a
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========================================<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]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</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 www
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