[gmx-users] .n2t file for ssDNA

[Justin A. Lemkul]

majid hasan wrote:
> I looked at the error in more detail (output attached), and it says 
> that: Warning: Residue T6 in chain has different type (Other) from 
> starting residue A1 (RNA). I had a dna.pdb file so first but its reading 
> the first residue as RNA.
> 
> So to me, problem seems to be that residues are named differently in my 
> dna.pdb file and dna.rtp file of force field. I looked at dna.pdb file 
> using more dna.pdb (output attached), and the residues are named as A, 
> C, G, T, while in Amber's dna.rtp file (attached) these are named as 
> DA3, DC3. Could this be a problem?  If this is, then how do I change the 
> names of residues in .pdb file, which I created it using a different 
> software (3DNA, and Gabedit)?
> 

The names of the residues must conform to the names found in the force field 
.rtp file.  The changes can be made with a text editor, but be careful not to 
shift the spacing of the .pdb file; its format must remain fixed.

-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
>  >
>  > ========================================
>  > -- gmx-users mailing list    gmx-users at gromacs.org 
> <mailto:gmx-users at gromacs.org> <mailto:gmx-users at gromacs.org 
> <mailto:gmx-users at gromacs.org>>
>>  http://lists.gromacs.org/mailman/listinfo/gmx-users
>>  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> 
> <mailto: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
> 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
> 
> ========================================
> -- gmx-users mailing list    gmx-users at gromacs.org 
> <mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> 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
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

========================================