[gmx-users] .n2t file for ssDNA
Justin A. Lemkul
jalemkul at vt.edu
Sat Apr 9 00:03:23 CEST 2011
majid hasan wrote:
> 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
Right, there are no nucleic acids in OPLS-AA by default. There may be
parameters out there somewhere, but they're not in Gromacs.
> 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.
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
> I also tried Amber, and Oplsaa forcefields on a different dna.pdb file,
> and got missing residue errors.
Then the input is not sound and thus is not a good test case.
> Any help would be much appreciated.
> *From:* Justin A. Lemkul <jalemkul at vt.edu>
> *To:* Discussion list for GROMACS users <gmx-users at 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
> > 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.
> > 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 <http://vt.edu> | (540) 231-9080
> -- gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> 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-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users