Thanks Justin! 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 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.
I also tried Amber, and Oplsaa forcefields on a different dna.pdb file, and got missing residue errors. Any help would be much appreciated. Thanks, Majid ________________________________ From: Justin A. Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Fri, April 8, 2011 12:54:38 PM Subject: Re: [gmx-users] .n2t file for ssDNA majid hasan wrote: > Dear All, > > I am trying to simulate the interaction between DNA, and CNT. But when I try > to >create the toplogy file with command > > 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 > > 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 > possible bonds in my .n2t file? > 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. 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. -Justin > I also downloaded the ffoplsaanr, ffoplsaano, from user contributed gromacs >forcefields, but these packages also don't have .n2t file. > > Thanks, > Majid > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists