[gmx-users] help with building DNA in gromacs

Tom dnaafm at gmail.com
Sun Jan 20 21:57:48 CET 2013


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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