[gmx-users] topology file for DNA molecule

Andrey V. Golovin golovin at genebee.msu.su
Thu Sep 30 08:15:01 CEST 2004

Hello Discussion,

9/30/2004, 8:15 AM you wrote:

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

This happened because OPLSA ff in gromacs doesn't contain any DNA/RNA
residues in rtp file. We added it and now busy with checking. Checking
is necessary because we added some dihedrals. I hope soon this files
can be found in contribution section.

tenghl> Thanks
tenghl> Hailong

Best regards,
Andrey                          mailto:golovin at genebee.msu.su

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