[gmx-users] .n2t file for ssDNA

majid hasan pu_majidhasan at yahoo.com
Sat Apr 9 00:41:36 CEST 2011 

Yes, of course. But right now I am just trying to make sure that my input files 
are all correct, and then I will dig into these actual forcefields.

Thanks a lot,
Majid



________________________________
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Gromacs Users' List <gmx-users at gromacs.org>
Sent: Fri, April 8, 2011 3:14:47 PM
Subject: Re: [gmx-users] .n2t file for ssDNA



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 <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 
>.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 <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>  > *To:* Discussion list for GROMACS users <gmx-users at gromacs.org 
><mailto: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 
>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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