majid hasan wrote:
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?
A force field should be chosen based on thorough study of the literature,
including the derivation of the parameter sets and their inherent assumptions
and limitations, as well as their success in reproducing relevant physical
observables. This is the most important choice you likely make when starting a
simulation, so you shouldn't simply choose a force field because it's there and
might "work" in terms of getting some form of output.
-Justin
Thanks,
Majid
------------------------------------------------------------------------
*From:* Justin A. Lemkul <jalem...@vt.edu>
*To:* Gromacs Users' List <gmx-users@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 .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 atoms.
> 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.
-Justin
> Any help would be much appreciated.
>
> Thanks,
> Majid
>
> ------------------------------------------------------------------------
> *From:* Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
> *To:* Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto: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 <http://vt.edu> <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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-- ========================================
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
========================================
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--
========================================
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
========================================
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