[gmx-users] .n2t file for ssDNA

[majid hasan]

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?

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>
> *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 
>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> | (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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