GROMACS modification: Yes/No
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I am doing an MD simulation of a peptide with 3 unnatural amino acids and a linker using Gromacs. I have already generated the itp files for unnatural amino acids and the linker using ATB web server.
Can anyone suggest to me how to generate topology(.itp and .top) for the whole peptide chain ?
If you have Itp files then you need to insert it to the top and create .gro file from the pdb. This is same as inserting ligand topology from protein-ligand simulation tutorial. On another way you can add the unnatural aminiacoid parameters int he respective files and invoke it hrough gmx pdb2gmx.
Thank you for your suggestion. May I know how can I unnatural amino acid parameters in the forcefield files ?
The only way to incorporate noncanonical residues into a contiguous polypeptide chain is to create
.rtp entries for those residues, add them to
residuetypes.dat as Protein residues, and add any necessary parameters to
ffnonbonded.itp (if necessary). I would contend that this approach has little to nothing to do with my protein-ligand tutorial, aside from potentially using external tools to help parametrize the new residues, but the use of a separate
.itp file for nonstandard species is not correct for this task.
Thank you @jalemkul . I got the point
Can anyone support me to get the accurate .hbd entry for the "HA’’ hydrogen in the attached molecule?
My following entry gives an error in Gromacs
I also want to know the “-C” meaning in .hbd entries
Addition type 5 requires 4 control atoms. See existing amino acids in the
.hdb file for how this is done.
The “-” prefix means the atom from the preceding residue in the polypeptide chain. Similarly, “+” means the next residue.