I am interested in DNA-protein MD. I have a custom made structure of a DNA motif, i have edited it (from ATGC to DA, DT, DG, DC) for gromacs and generated topology using amber99sb-ildn.ff.
After that i followed the steps for protein-ligand docking
(as mentioned in tutorial at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex). There were no errors, but now at grompp step i am stuck and getting
Fatal error:
No such moleculetype DNA
what i understand that it is not reading my DNA molecule or some how it is unavailable for the program. Do i need to modify the .rtp file or edit the residue name?
It looks that you run pdb2gmx for different parts of your system separately. Your topology is not correct.
In the *top file, there is a [ molecules ] directive. This contains the information about actual parts system This should list only items that have an appropriate [ moleculetype ] directive. All the parts (*itp) should also be linked with the *top.
Please check that your *top contains something like "#include 'path/to/dna.itp'"
Depending on the exact situation with your topology, you may check the *itp file of the nucleic acid, and change the first word to "DNA".
See Sec 5.8.2 of the Gromacs manual 2016.2 (http://manual.gromacs.org/documentation/2016.2/manual-2016.2.pdf).
Which force field are you using?
Also, Check the path mentioned in the topology.top file and include the path of your .itp file.
Hi, I agree with the above. The first step if you want to introduce a new molecule is to add it (by name) to your ff rtp file of your choice
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