[gmx-users] help with building DNA in gromacs

יוכבד ybaime at gmail.com
Wed Jan 23 09:56:51 CET 2013

Hi Steven

I'm running simulations on DNA structures using the amber99sb-ildn FF. I
had no problem generating .top and .gro files
I might be able to help if you are interested.
send me the PDB file.


On Sun, Jan 20, 2013 at 10:57 PM, Tom <dnaafm at gmail.com> 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?
> Is there any toolbox to help buld the top file?
> Thanks,
> Steven
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