Hello everyone,
I found a script written by Daniel R. Roe (
https://github.com/drroe/AmberMdPrep) that is designed to implement a reliable protocol for MD simulations (DOI: 10.1063/5.0013849). I am studying the interactions between a B-DNA dodecamer (PDB ID: 1BNA) and a metalloorganic complex parameterized by MCPB.py, inserting the complex between different DNA pairs. Surprisingly, all the jobs finish in the first cycle of the final step, with the .out and .results files similar to the example given here:
https://justpaste.it/driau .
Could someone kindly confirm whether the jobs have terminated correctly according to the script’s requirements? Perhaps I overlooked something, considering the presence of DNA and my own ligands (e.g., incorrect residue names?). An example of the input for AmberMdPrep.sh looks like this:
./AmberMdPrep.sh -p ATTA_solv.prmtop -c ATTA_solv.inpcrd --mask ":25-27&!.H=" --ares "BP1,BP2,CU1" --temp 300 --nprocs 28 --type nucleic
where BP1, BP2, and CU1 are parts of my organometallic complex, and 25-27 are their corresponding residues.
Thanks in advance !
–
Maciej Spiegel, MPharm PhD
assistant professor
Department of Organic Chemistry and Pharmaceutical Technology,
Faculty of Pharmacy, Wroclaw Medical University
Borowska 211A, 50-556 Wroclaw, Poland
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Received on Sat Aug 17 2024 - 14:00:03 PDT
