if there is an amber command line for that, how will it look like because the one i used made both peptides overlap
I think that should be done before simulation system preparation. Use a protein structure viewer such as chimera or Schrodinger Maestro (free academic version), then perform the following steps
1. Combine both the structures to a single workspace entry
2. Select the entry or Chain name then move accordingly to a close proximity so that no atom overlaps or clashes.
3. Rename the proteins chains if required
4. Finally, export to a single PDB file
Then you are ready to generate a simulation system with both the proteins.
gmx insert-molecules might be one of the easiest way to do that. Otherwise, you can use vmd or Pymol.
To put two independent protein structures in a single solvent box without any overlap using the Amber command line, you can follow these steps:
Jamoliddin Razzokov thank you for responding. i actually did that before now and got this error message
"solvateBox: Argument #1 is type List must be of type: [unit]
usage: solvateBox [iso] [closeness]
Exiting LEaP: Errors = 1; Warnings = 0; Notes = 0."
Yanxing Yang i was able to space both peptides using vmd but the challenge is the difficulty in generating parameter and top[ology files for the spaced combined protein/peptide. i am encountering multiple errors using tleap tool
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