[gmx-users] topology file for DNA molecule

tenghl hailong at seas.ucla.edu
Thu Sep 30 06:15:32 CEST 2004

Dear Gromacs users, 
I am trying to build a topology file for a DNA model using pdb2gmx -f file.pdb -p file.top -o file.gro.
I used OPLS force field and got the following error, any ideas? 
Sorting it all out...
Opening library file /space/gromacs/share/top/ffoplsaa.hdb
Opening library file /space/gromacs/share/top/ffoplsaa-n.tdb
Opening library file /space/gromacs/share/top/ffoplsaa-c.tdb
Processing chain 1 (438 atoms, 20 residues)
Opening library file /space/gromacs/share/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Fatal error: Residue 'A5' not found in residue topology database



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20040929/10ee5c8e/attachment.html>

More information about the gromacs.org_gmx-users mailing list