<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>Okay, thanks, I'll stick to Amber then.</div><div><br></div><div>Thanks again,</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> Sun, April 17, 2011 6:35:07 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] .top file for DNA-CNT<br></font><br>
<br><br>majid hasan wrote:<br>> Okay, so I just removed #include forcefield from top, and [system] [molecule] directives from the bottom of my topology file, and saved it as .itp file. Is that fine? <br><br>Yes.<br><br>> And, if I #include water topology in dna.itp file, then I shouldn't include it in system's topology file, and it doesn't make any difference whether I include water in a molecule.itp file or I add it explicitly in system topology, right?<br>> <br><br>Correct. I often find it much simpler to just #include everything in one .top file rather than having unnecessary nested #includes, but do what makes the most sense for yourself.<br><br>> Moreover, I created cnt.top using oplsaa forcefield, so in my cnt.itp file carbon atoms' "type" is opls_240. So when I run the grompp using amber99sb-ildn, it gives me the following error: Fatal Error: Atomtype opls_240 not found, which is probably because amber doesn't recognize
opls_240.<br>> <br><br>Never mix and match force fields. You must have one self-consistent representation of the system.<br><br>> How should I correct the atom type in my cnt.itp file? If I just add an atomtype opls_240 in /amber99sb-ildn.ff/atomtypes.atp, would it be enough? Manual's section 5.8.3 says that "after definition of new atom <br><br>No. You can't simply append one force field's content to another and hope it works. You may be able to form a syntactically correct force field, but it would be a complete hack job that would not give anything close to a reliable simulation.<br><br>> types, additional non-bonded, and pair parameters can be defined." I earlier added some CNT parameters ([bond types], [angle types], ..) in ffoplsaabon.itp, do I need to make exactly the same changes in amber.ff/ffbonded.itp?<br>> <br><br>Leave these files alone. There is no need to alter them in this case.<br><br>> Is it
generally not possible to create topology of one molecule using one forcefield, and then do MD simulation of entire system using another forcefield (without changing parameters etc.)?<br>> <br><br>In general, no, force fields cannot be combined in this way. There are limited exceptions, but this case is not one of them. You need to choose a parent force field that is suitable for all components of your system and derive molecule topologies from this force field. Mixing and matching will be a great way to waste time.<br><br><span><a target="_blank" href="http://www.gromacs.org/Documentation/How-tos/Parameterization">http://www.gromacs.org/Documentation/How-tos/Parameterization</a></span><br><br>-Justin<br><br>> Thanks for your help,<br>> Majid<br>> ------------------------------------------------------------------------<br>> *From:* Justin A. Lemkul <<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>><br>> *Sent:* Sun, April 17, 2011 4:54:11 PM<br>> *Subject:* Re: [gmx-users] .top file for DNA-CNT<br>> <br>> <br>> <br>> majid hasan wrote:<br>> > Dear All,<br>> ><br>> > I want to simulate DNA-CNT interaction, and reproduce the helical wrapping of DNA around CNT in the first step, and later study the effects of temperature, CNT length etc on the favorable geometries of hybrid.<br>> ><br>> > I have created .top files for DNA, and CNT separately. To generate the top file of entire system (DNA-CNT), I added CNT in a box with DNA using genbox. But when I try to create .top file using pdb2gmx and Amber forcefield, I get an error that atom C in residue 11 C not found in
rtp entry because rtp because .rtp file in Amber only contain dna residues, and if I use some other forcefield like oplsaa then dna residues won't be present. So how do I create the .top file for whole system i.e DNA-CNT?<br>> ><br>> > Mailing list suggests that another and probably easier way of doing this is to create .itp file for CNT, and add it to dna.top file using #include file mechanism. So I wanted to ask how can I create .itp file from topology file (because I have the toplogy file for CNT), or do I need to create it manually from scratch?<br>> ><br>> <br>> The conversion of .top to .itp is simple. A .top is a system topology and contains a description of the entire system. An .itp file describes one type of molecule. To create a .itp from a .top, follow this:<br>> <br><span>> <a target="_blank"
href="http://www.gromacs.org/Documentation/File_Formats/.itp_File">http://www.gromacs.org/Documentation/File_Formats/.itp_File</a></span><br>> <br>> Then a simple system topology is just:<br>> <br>> #include (whatever force field)<br>> #include "cnt.itp"<br>> #include "dna.itp"<br>> #include "spc.itp" (or whatever water)<br>> #include "ions.itp" (if needed)<br>> <br>> Finish with appropriate [system] and [molecules] directives.<br>> <br>> -Justin<br>> <br>> > Thank You,<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>> | (540) 231-9080</span><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>><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> <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
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