Hello,
you might want to check the tutorials on the Amber website
(
https://ambermd.org/tutorials/).
Best,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 23.06.2025 um 11:27 schrieb Md Imran Ahmed via AMBER:
> 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:
>
>> Send AMBER mailing list submissions to
>> amber.ambermd.org
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> http://lists.ambermd.org/mailman/listinfo/amber
>> or, via email, send a message with subject or body 'help' to
>> amber-request.ambermd.org
>>
>> You can reach the person managing the list at
>> amber-owner.ambermd.org
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of AMBER digest..."
>>
>>
>> AMBER Mailing List Digest
>>
>> 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
>>
>>
>> ------------------------------
>>
>> Subject: Digest Footer
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>> ------------------------------
>>
>> End of AMBER Digest, Vol 4731, Issue 1
>> **************************************
>>
> _______________________________________________
> 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 Mon Jun 23 2025 - 04:00:03 PDT
