Hi,
Do you see any of the following in the output from AmberMdPrep.sh?
ADD. MASK RES. : BP1,BP2,CU1
Detected additional res mask: :BP1,BP2,CU1&!.H=
It should also show up in the 'restraintmask' namelist variables in
your individual step input files (step1.in etc).
-Dan
On Mon, Aug 19, 2024 at 3:08 PM Maciej Spiegel
<maciej.spiegel.umw.edu.pl> wrote:
>
> Alright. In my initial inquire, I also referred to the "--mask and "--ares flags. While the former seems to be working since the relevant „restraintmask" entries are present in the generated „.in" files, the "--ares flag appears to be ignored. Could this be because I specify parts not recognized by cpptraj, which in cosequence would also explain why the tmp.unknownResNames file is listing them? I'm particularly curious about this because, in addition to the MCPB.py-parameterized complex, it also lists Na+ ions.
>
> Best,
> –
> 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
>
> Wiadomość napisana przez Daniel Roe via AMBER <amber.ambermd.org> w dniu 19.08.2024, o godz. 15:01:
>
> Hi,
>
> On Mon, Aug 19, 2024 at 8:45 AM Maciej Spiegel
> <maciej.spiegel.umw.edu.pl> wrote:
>
> I asked about that because, in your previous message, you stated that starting production simulations "would feel OK." This sounded ambiguous to me, as if the production is not actually being carried out.
>
>
> So I intentionally used more general language because I know nothing
> about your simulations, the system, your goals, etc. The protocol as
> stated in the paper is just for the initial relaxation of the system
> so you e.g. don't get catastrophic forces that can blow the simulation
> up. It doesn't necessarily guarantee everything is ready for
> production. For example, if ion redistribution is important, 1 ns
> might not be enough time for that to have occurred. So while I can't
> say for certain that your system is ready for whatever production
> phase, I am fairly confident you won't get any 'VLIMIT' errors going
> forward. :-)
>
> -Dan
>
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Received on Mon Aug 19 2024 - 13:00:02 PDT
