Do the residues not show up in any of the other input files? If not, I’m
not sure why, but it doesn’t seem to have negatively impacted the
relaxation.
On Mon, Aug 19, 2024 at 3:10 PM Maciej Spiegel <maciej.spiegel.umw.edu.pl>
wrote:
>
> Hey,
>
> This is what the script yields:
>
> AmberMdPrep.sh Version 0.5 (beta)
> TOP : ATTA_solv.prmtop
> CRD : ATTA_solv.inpcrd
> 0 protein, 24 dna, 0 rna, 0 lipid, 0 carbohydrate, 8790 water, 24 other
> Unknown residues names: BP1,BP2,CU1,Na+
> Warning: Unknown residues detected; will be ignored for restraints.
> Detected types : nucleic
> NUM SOLUTE RES : 24
> HEAVY MASK : :1-24&!.H=
> BACKBONE MASK : :1-24.P,O5',C5',C4',C3',O3'
> ADDITIONALMASK : :25-27&!.H=
> ADD. MASK RES. : BP1,BP2,CU1
> TEMPERATURE : 300
> OVERWRITE : 0
> MD COMMAND : mpirun -n 28 pmemd.MPI
> MIN COMMAND : mpirun -n 28 pmemd.MPI
> NPROCS : 28
>
> Performing standard min/equil
> Minimization: step1
> MD: step2
>
>
>
> ...for the submission as:
>
> ./AmberMdPrep.sh -p ATTA_solv.prmtop -c ATTA_solv.inpcrd --mask
> ':25-27&!.H=' --ares 'BP1,BP2,CU1' --temp 300 --nprocs 28 --type nucleic
>
>
>
> ...and so step1.in generated looks like that:
>
> Minimization: step1.in
> &cntrl
> imin = 1, ntmin = 2, maxcyc = 1000, ncyc = 10,
> ntwx = 500, ioutfm = 1, ntxo = 2, ntpr = 50, ntwr = 500,
> ntc = 1, ntf = 1, ntb = 1, cut = 8.0,
> ntr = 1, restraintmask = ":1-24&!.H=|:25-27&!.H=", restraint_wt = 5.0,
> &end
>
>
> …but the file „tmp.unknownResNames” is still created. Apparently it
> doesn’t recognize them by name but by mask.
>
> Best,
> –
> Maciej Spiegel, MPharm PhD
> *assistant professor*
>
> *Department of Organic Chemistry **and **Pharmaceutical Technology,*
> *Faculty of Pharmacy, **Wroclaw Medical University*
> *Borowska 211A,
> <https://www.google.com/maps/search/Borowska+211A,+50-556+Wroclaw,+Poland?entry=gmail&source=g> **50-556
> Wroclaw, Poland
> <https://www.google.com/maps/search/Borowska+211A,+50-556+Wroclaw,+Poland?entry=gmail&source=g>*
>
> Wiadomość napisana przez Daniel Roe <daniel.r.roe.gmail.com> w dniu
> 19.08.2024, o godz. 21:36:
>
>
> 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
> <https://www.google.com/maps/search/Borowska+211A,+50-556+Wroclaw,+Poland?entry=gmail&source=g>
>
>
> 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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>
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>
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>
>
>
>
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Received on Mon Aug 19 2024 - 15:00:02 PDT
