[gmx-users] .n2t file for ssDNA

majid hasan pu_majidhasan at yahoo.com
Fri Apr 8 23:58:35 CEST 2011

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 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.

I also tried Amber, and Oplsaa forcefields on a different dna.pdb file, and got 
missing residue errors. 

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 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.


> 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

-- gmx-users mailing list    gmx-users at gromacs.org
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.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110408/09e50b00/attachment.html>

More information about the gromacs.org_gmx-users mailing list