[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?



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