<div id="RTEContent">Here it is<br>http://folding.stanford.edu/ffamber/<br><br><b><i>Ken Rotondi <ksr@chemistry.umass.edu></i></b> wrote:<blockquote class="replbq" style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"> On Jan 25, 2006, at 3:54 AM, David van der Spoel wrote:<br><br>> On Tue, 24 Jan 2006, Ken wrote:<br>><br>>> Hello all,<br>>><br>>> I've processed an RNA chain in GROMACS 3.2.1 using the G43a1 ff<br>>> to .gro and .top files. Upon trying to generate a .tpr file for<br>>> genion, grompp returned an series of warnings leading to a fatal<br>>> error, eg.:<br>>><br>><br>> this is proibably not the answer you want, but try the amber force <br>> field<br>> with gromacs 3.3 (ff available from the contribution section)<br><br>There is no way to fix this? It seem as though it should be a trivial <br>matter of adding a definition to a ff file.<br><br>In searching the contributions
section of the GROMACS site I find the <br>only references to AMBER are in the AMBCONV utility to change AMBER <br>topologies and coordinate files to GROMACS .gro and .top files. <br>Searching the site for AMBER returns one hit from Berk Hess detailing <br>revisions to 3.3 that concerns AMBCONV. Where is this force field?<br><br>Is this a UA ff or and AA ff? I need a UA ff due to the system size. If <br>this flavor of AMBER is AA then I cannot use it.<br><br>><br>><br>>> WARNING 2 [file "rnatest.top", line 605]:<br>>> No default Proper Dih. types, using zeroes<br>>><br>>> looking at the .top file line 605 I find:<br>>><br>>> [ dihedrals ]<br>>> ; ai aj ak al funct c0 c1<br>>> c2 c3 c4 c5<br>>> 2 1 4 5 1<br>>> 1 4 5 6 1 gd_14<br>>><br>>> Which indicates that GROMACS does not know how to assign
the O1P-P-<br>>> O5*-C5* proper dihedral in the RNA backbone, as this dihedral is<br>>> blank for every nucleotide.<br>>><br>>> Unfortunately the example .top file in the 3.2 manual has a different<br>>> format,<br>>><br>>> [ dihedrals ]<br>>> ; ai aj ak al funct phi cp mult<br>>> 2 1 3 4 1 1.800000e+02 3.347200e+01 2.000000e+00<br>>><br>>> and a search of the manual for gd_14 (seemed like a good place to<br>>> start) returned nothing.<br>>><br>>> What is the correct dihedral type for these atoms? How can I modify<br>>> GROMACS to assign these correctly?<br>>><br>>> Many thanks,<br>>><br>>> Ken<br>>><br>>><br>><br>> -- <br>> David.<br>> _______________________________________________________________________ <br>> _<br>> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>> Dept. of Cell and Molecular Biology, Uppsala
University.<br>> Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>> phone: 46 18 471 4205 fax: 46 18 511 755<br>> spoel@xray.bmc.uu.se spoel@gromacs.org http://xray.bmc.uu.se/~spoel<br>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ <br>> +<br>><br>> _______________________________________________<br>> gmx-users mailing list<br>> gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to gmx-users-request@gromacs.org.<br><br>_______________________________________________<br>gmx-users mailing list<br>gmx-users@gromacs.org<br>http://www.gromacs.org/mailman/listinfo/gmx-users<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br></blockquote><br></div>