Hi
I need to build psf of m7G capped rna structure (pdb id-6IS0). The m7G is unrecognizable by topology file. Can anyone please help me in building psf of this whole structure. I can't find tutorial anywhere on how to build topology file.
You get most of the answers you need by simply googling e.g. "topology file generator" and follow the most interesting amongst the first few hits to find several servers and collections of topology and parameter files (look at the "help and faq files for details on how to use them)
The PDB format does not sufficiently describe your compound, as it does not contain any information about bond orders, charges and usually does not contain the hydrogens. To generate a topology file, you need to provide the coordinates in a format that completely describes its chemical structure https://www.rcsb.org/ligand/M7G - if you download 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE as pdf file, you get the structure including double bonds and hydrogen positions
Did you add hydrogens to your HETATM?
e.g. gromacs gmx x2top https://manual.gromacs.org/archive/5.0/programs/gmx-x2top.html
gmx x2top generates a primitive topology from a coordinate file. The program assumes all hydrogens are present when defining the hybridization from the atom name and the number of bonds. The program can also make an .rtp entry, which you can then add to the .rtp database.
e.g from Automated Topology Builder (ATB) and Repository Version 3.0 https://atb.uq.edu.au/index.py?tab=faq
Can I submit a ligand (heteromolecule) molecule as is from a PDB file?
No. The ligand molecules in most PDB files only contain HEAVY ATOMS. The complete ligand molecule (with all HYDROGEN atoms and correct tautomeric and protonation states as well as its formal charge) must be submitted to the ATB. Only then isit possible for the ATB to generate a complete topology file. A range of programs such as ArgusLab or Avogadro can be used to edit the hydrogen atoms in a ligand molecule.
The answer also depends on which forcefield you are using, as the parameter and topology files have to match the forcefield you are using, therefore restrict your search accordingly
Topology file tutorials (searching for "topology file tutorial" , add the specific force field / program you are using to get more specific answers ):
e.g.
http://www.ks.uiuc.edu/Training/Tutorials/science/topology/topology-tutorial.pdf
https://cupdf.com/document/topology-file-tutorial-illinois-in-molecular-dynamics-simu-lations-this-molecule.html?page=1
Lesson 2: Topology Files
https://charmm-gui.org/?doc=lecture&module=molecules_and_topology&lesson=2
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Preparing_an_AMBER_topology_file_for_a_protein_system
I did not read all of them, but learn to do specific web searches to get your answers quickly without having to wait for a real person to answer to that they think is your problem
I think I can pick up smoothly from here . thank you so much Annemarie Honegger
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