[gmx-users] Residue problem in DNA

Yinghong xieyh at hkusua.hku.hk
Fri Feb 13 04:17:01 CET 2004

Dear gmx users:
While simulating DNA molecules via Gromacs, a fatal error always happened, that is "Residue xxx not found in the residue topology database".
Actually, I know that the residue name in the .pdb file must be the same as ff***.rtp, so I modified these files by 'sed' command, either
Just changing the A C G T residues in the original pdb file to DADE, DCYT, DGUA, DTHY, and the latter is the same as those in ff***.rtp files;
Only changing the DADE, DCYT, DGUA, DTHY in the ff***.rtp to A C G T as presented in the pdb files.
Anyway, the purpose of these modifications is to make residue names  be the same between pdb and ff***.rtp files. However, all of these could not yet work well, and the error "Residue xxx not found in the residue topology database" is still emerged.
Therefore, I am now quite confused, and also hope your help!

Thanks in advance.

Xie YH
The University of Hongkong
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