[gmx-users] .n2t file for ssDNA
pu_majidhasan at yahoo.com
Sat Apr 9 00:12:18 CEST 2011
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?
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Gromacs Users' List <gmx-users at gromacs.org>
Sent: Fri, April 8, 2011 3:03:23 PM
Subject: Re: [gmx-users] .n2t file for ssDNA
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
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 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
> > 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
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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