[gmx-users] help with building DNA in gromacs

Justin Lemkul jalemkul at vt.edu
Sun Jan 20 22:01:15 CET 2013

On 1/20/13 3:57 PM, Tom wrote:
> Dear Gromacs User
> I built DNA with the pdb file and *mol2
> But when I used pdb2gmx to obtain *top file, pdb2gmx give error
> report when I chose charmm27:
> ---------------------------
> Program pdb2gmx, VERSION 4.5.5
> Source code file: resall.c, line: 581
> Fatal error:
> Residue 'T' not found in residue topology database
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------
> Also can not work for the other forcefileds.
> Why for simple DNA is so difficult to build topology file?

Your residue names need to match the force field's expectations.  That much is 
true for any molecule passed to pdb2gmx - protein, DNA, RNA, whatever.  Consult 
the .rtp file for your chosen force field and edit your coordinate file accordingly.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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