Hello all ,i am new to this field in computational chemistry and i want to
learn md simulation using AMBER,i am finding it difficult to learn it from
the manually as all the steps are given differently can somebody help me
with the tutorial part please.
On Tue, Jun 17, 2025 at 12:31 AM <amber-request.ambermd.org> wrote:
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> Today's Topics:
>
> 1. Number of frames loaded in doing MMPBSA.py (Jong Young Joung)
> 2. Fwd: Number of frames loaded in doing MMPBSA.py (Jong Young Joung)
> 3. Re: Fwd: Number of frames loaded in doing MMPBSA.py
> (Bill Miller III)
> 4. Building double bilayer using packmol-memgen (Cherry, Kendall)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 16 Jun 2025 15:49:50 +0900
> From: Jong Young Joung <jongyoung.joung.gmail.com>
> To: amber.ambermd.org
> Subject: [AMBER] Number of frames loaded in doing MMPBSA.py
> Message-ID:
> <
> CAGZT7tNVgu0Lk-0ZRbQSU1NSKBxoWRbP8BSk+fKH_LQrAo0icQ.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi all,
>
> After performing 100 ns simulations, in which frames are stored every 10 ps
> , I extracted a portion of the trajectories with the specified frame ids.
> When I loaded the crd file that has 150 frames, only 10 frames were
> processed during the MMPBSA procedures.
> It looks that automatically, every 15 frames were loaded in the MMPBSA
> calculation from the input crd file.
> In the MMPBSA input file (mmpbsa.in), I assigned the "interval" option as
> 1.
>
> [mmpbsa.in]
> input for mmpbsa
> &general
> startframe=1,
> interval=1,
> entropy=0,
> receptor_mask=:1-288,
> /
> &gb
> igb=5,
> /
>
> This is my md option.
> [md.in]
> md run
> &cntrl
> imin=0,
> irest=0,
> ntx=5,
> ntb=1,
> cut=12.0,
> ntr=0,
> ntc=2, ntf=2,
> ntt=3, gamma_ln = 1.0,
> nstlim=5000000,
> dt=0.002,
> ntpr=5000,
> ntwx=5000,
> ntwr=500000,
> /
>
> Did I miss anything to include all the frames from the input crd file to
> the mmpbsa?
>
> Many thanks in advance,
>
> jongyoung
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 16 Jun 2025 16:10:53 +0900
> From: Jong Young Joung <jongyoung.joung.gmail.com>
> To: amber.ambermd.org
> Subject: [AMBER] Fwd: Number of frames loaded in doing MMPBSA.py
> Message-ID:
> <
> CAGZT7tP5uyYyT_bF+5Wr115_VQDTfcNO-4hAT-q4UPd_CqStvw.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi all,
>
> After performing 100 ns simulations, in which frames are stored every 10 ps
> , I extracted a portion of the trajectories with the specified frame ids.
> When I loaded the crd file that has 150 frames, only 10 frames were
> processed during the MMPBSA procedures.
> It looks that automatically, every 15 frames were loaded in the MMPBSA
> calculation from the input crd file.
> In the MMPBSA input file (mmpbsa.in), I assigned the "interval" option as
> 1.
>
> [mmpbsa.in]
> input for mmpbsa
> &general
> startframe=1,
> interval=1,
> entropy=0,
> receptor_mask=:1-288,
> /
> &gb
> igb=5,
> /
>
> This is my md option.
> [md.in]
> md run
> &cntrl
> imin=0,
> irest=0,
> ntx=5,
> ntb=1,
> cut=12.0,
> ntr=0,
> ntc=2, ntf=2,
> ntt=3, gamma_ln = 1.0,
> nstlim=5000000,
> dt=0.002,
> ntpr=5000,
> ntwx=5000,
> ntwr=500000,
> /
>
> Did I miss anything to include all the frames from the input crd file to
> the mmpbsa?
>
> Many thanks in advance,
>
> jongyoung
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 16 Jun 2025 06:39:10 -0500
> From: Bill Miller III <brmilleriii.gmail.com>
> To: Jong Young Joung <jongyoung.joung.gmail.com>, AMBER Mailing List
> <amber.ambermd.org>
> Subject: Re: [AMBER] Fwd: Number of frames loaded in doing MMPBSA.py
> Message-ID: <3EA143AB-09AF-4434-AEB9-0A9155D2ADA2.gmail.com>
> Content-Type: text/plain; charset=utf-8
>
> No, I don?t think you?re missing anything. The interval=1 variable is
> telling MMPBSA.py to read every frame in the input trajectory. That
> suggests your issue occurs before then. When you process the same
> trajectory with cpptraj, does it suggest more frames?
>
> -Bill
>
>
>
> > On Jun 16, 2025, at 2:14?AM, Jong Young Joung via AMBER <
> amber.ambermd.org> wrote:
> >
> > ?Hi all,
> >
> > After performing 100 ns simulations, in which frames are stored every 10
> ps
> > , I extracted a portion of the trajectories with the specified frame ids.
> > When I loaded the crd file that has 150 frames, only 10 frames were
> > processed during the MMPBSA procedures.
> > It looks that automatically, every 15 frames were loaded in the MMPBSA
> > calculation from the input crd file.
> > In the MMPBSA input file (mmpbsa.in), I assigned the "interval" option
> as 1.
> >
> > [mmpbsa.in]
> > input for mmpbsa
> > &general
> > startframe=1,
> > interval=1,
> > entropy=0,
> > receptor_mask=:1-288,
> > /
> > &gb
> > igb=5,
> > /
> >
> > This is my md option.
> > [md.in]
> > md run
> > &cntrl
> > imin=0,
> > irest=0,
> > ntx=5,
> > ntb=1,
> > cut=12.0,
> > ntr=0,
> > ntc=2, ntf=2,
> > ntt=3, gamma_ln = 1.0,
> > nstlim=5000000,
> > dt=0.002,
> > ntpr=5000,
> > ntwx=5000,
> > ntwr=500000,
> > /
> >
> > Did I miss anything to include all the frames from the input crd file to
> > the mmpbsa?
> >
> > Many thanks in advance,
> >
> > jongyoung
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 16 Jun 2025 16:28:33 +0000
> From: "Cherry, Kendall" <kche.email.unc.edu>
> To: "amber.ambermd.org" <amber.ambermd.org>
> Subject: [AMBER] Building double bilayer using packmol-memgen
> Message-ID:
> <
> PH0PR03MB57816E74E3F0AA9CA73152269F70A.PH0PR03MB5781.namprd03.prod.outlook.com
> >
>
> Content-Type: text/plain; charset="us-ascii"
>
> Hello,
>
> I work with membrane proteins and am interested in creating a double
> bilayer system to study ion flux through the protein. I have successfully
> built a single bilayer system using packmol-memgen, but when I add the
> computational electrophysiology flags (--double --charge_imbalance 2
> --imbalance_ion cat), I get this error:
>
> Traceback (most recent call last):
> File "/proj/pierilab/software/amber/amber24/bin/packmol-memgen", line
> 193, in <module>
> pmg.run_all()
> File
> "/proj/pierilab/software/amber/amber24/lib/python3.12/site-packages/packmol_memgen/main.py",
> line 2005, in run_all
> pack = self.prepare()
> ^^^^^^^^^^^^^^
> File
> "/proj/pierilab/software/amber/amber24/lib/python3.12/site-packages/packmol_memgen/main.py",
> line 1358, in prepare
> solvent_vol_up =
> (X_len*Y_len*(abs(Z_dim[bilayer][1])-leaflet_z))-solvol[bilayer][1]
>
> ~~~~~~^^^^^^^^^
> IndexError: list index out of range
>
> I have reproduced this error with the --double flag alone, so it is not
> due to the --charge_imbalance or --imbalance_ion flags. I also have tried
> changing the dimensions of the box (either --distxy_fix 75 --dist_wat 25 or
> --dims 75 75 200 ) just to see if that fixes this issue, but it does not.
> This is my full packmol-memgen command:
> packmol-memgen --pdb LLLL_tleap.pdb --lipids POPC --dims 75 75 200
> --random --nloop 30 --salt --keepligs --ffwat opc --ffprot ff19SB
> --notprotonate --nottrim --double
>
> I would welcome help from anyone who knows packmol-memgen better than I
> do, and/or anyone who has successfully built a double bilayer system!
>
> Thank you,
> Kendall Cherry
>
> Chemistry Ph.D. Student
> University of North Carolina at Chapel Hill
>
>
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> ------------------------------
>
> End of AMBER Digest, Vol 4731, Issue 1
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Received on Mon Jun 23 2025 - 03:00:02 PDT
