[gmx-users] Residue problem in DNA

[Anton Feenstra]

Yinghong wrote:

> 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;
> or
> 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!

Some of these things are hardcoded in pdb2gmx. You should check if pdb2gmx
recognizes your molecules as DNA, it will print a list of what types of
molecules it finds: protein, nucl.acid, water, other. So, in fact, residue
names in the .rtp and the .pdb file must match what pdb2gmx expects!
Which forcefield are you using?


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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