Hi,
Check the Eval.agr plot of system density vs time and the values in
Eval.results to make certain everything looks OK, but it’s not unusual for
systems to be finished within the first final phase. If you check the
accompanying paper you’ll see that the average time it took for the system
density to “flatten out” was around 175 ps, so the default value of 1 ns
was chosen so that most systems would be “done” at that point (only 3 of
the systems I tested needed longer than that).
So unless something looks weird to you everything might be ok. Let me know
if I’m not understanding your issue correctly.
-Dan
On Sat, Aug 17, 2024 at 5:03 PM Maciej Spiegel via AMBER <amber.ambermd.org>
wrote:
> 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
> <https://www.google.com/maps/search/Borowska+211A,+50-556+Wroclaw,+Poland?entry=gmail&source=g>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Aug 17 2024 - 16:00:01 PDT
