Just skip the NMA calculation, which doesn’t improve correlation with experiment anyways, and use a second-order cumulant of your interaction energy. See
https://pubs.acs.org/doi/10.1021/acs.jctc.8b00418 <
https://pubs.acs.org/doi/10.1021/acs.jctc.8b00418>.
David Minh, PhD
Assistant Professor, Department of Chemistry
Associate Director, Center for Interdisciplinary Scientific Computation
Illinois Institute of Technology
email: david.minh.iit.edu <mailto:david.minh.iit.edu>
Skype: daveminh
Links:
Research group <
http://mypages.iit.edu/~dminh/>
David’s availability calendar <
https://calendar.google.com/calendar/embed?src=daveminh@gmail.com&ctz=America/Chicago>
> On Feb 18, 2019, at 2:00 PM, amber-request.ambermd.org wrote:
>
> Send AMBER mailing list submissions to
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>
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> When replying, please edit your Subject line so it is more specific
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>
> AMBER Mailing List Digest
>
> Today's Topics:
>
> 1. Fwd: making force fields files from topology (Hadi Rahmaninejad)
> 2. Fwd: making force fields files from topology (Hadi Rahmaninejad)
> 3. peptide-bilayer MD simulation analysis (golshan bakrani)
> 4. Speed-up calculation of Entropy with MMPBSA (James Starlight)
> 5. Umbrella Sampling and WHAM analysis (mish)
> 6. Re: Speed-up calculation of Entropy with MMPBSA (David A Case)
> 7. Re: making force fields files from topology (David A Case)
> 8. Re: MMPBSA (David A Case)
> 9. MBAR from TI on pmemd (Hosein Geraili Daronkola)
> 10. Re: Amber18 TI on K10 - any known problem? (David A Case)
> 11. Re: Interpreting QM MMPBSA results (David A Case)
> 12. Re: Speed-up calculation of Entropy with MMPBSA (James Starlight)
> 13. Re: MMPBSA (Nisha Amarnath Jonniya)
> 14. ChamberParm objects are not supported by this action
> (Hadi Rahmaninejad)
> 15. puckering coordinates (MYRIAN TORRES RICO)
> 16. Re: ChamberParm objects are not supported by this action
> (David A Case)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 17 Feb 2019 18:22:21 -0500
> From: Hadi Rahmaninejad <ha.rahmaani.gmail.com>
> Subject: [AMBER] Fwd: making force fields files from topology
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CABZiX_SOJWYwy8YCDrnhKCMOCpem+1HVn2HTHf+YFRbistxeWg.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> ---------- Forwarded message ---------
> From: Hadi Rahmaninejad <ha.rahmaani.gmail.com>
> Date: Thu, Feb 14, 2019 at 10:31 AM
> Subject: making force fields files from topology
> To: AMBER Mailing List <amber.ambermd.org>
>
>
> Hello Amber Users,
>
> We know that we can easily create topology and coordinate from forcefields
> files (frcmod and prep files) using tleap or xleap. But, in my case, I have
> topology and coordinate files of system getting from "Parmed", and need to
> obtain forcefield files (to change the solvation). Is there any possibility
> to get forcefield files from topology and coordinate files of system in
> amber?
>
> Thank you in advance,
> Best regards,
> Hadi
>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 17 Feb 2019 18:28:06 -0500
> From: Hadi Rahmaninejad <ha.rahmaani.gmail.com>
> Subject: [AMBER] Fwd: making force fields files from topology
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CABZiX_SAWWF-16ibdNMhg+6z6FKg4AZFO-=+=xGHDWWSReKmyw.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> ---------- Forwarded message ---------
> From: Hadi Rahmaninejad <ha.rahmaani.gmail.com>
> Date: Thu, Feb 14, 2019 at 10:31 AM
> Subject: making force fields files from topology
> To: AMBER Mailing List <amber.ambermd.org>
>
>
> Hello Amber Users,
>
> We know that we can easily create topology and coordinate from forcefields
> files (frcmod and prep files) using tleap or xleap. But, in my case, I have
> topology and coordinate files of system getting from "Parmed", and need to
> obtain forcefield files (to change the solvation). Is there any possibility
> to get forcefield files from topology and coordinate files of system in
> amber?
>
> Thank you in advance,
> Best regards,
> Hadi
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 18 Feb 2019 09:20:35 +0330
> From: golshan bakrani <golshan7193.gmail.com>
> Subject: [AMBER] peptide-bilayer MD simulation analysis
> To: amber.ambermd.org
> Message-ID:
> <CAD5S2aiWiepLrK-i2Ri8HHkiOniad5NN+NGeV0VkezjgPUoEhw.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear Amber community,
>
> I performed MD simulation on a peptide in interaction with bilayer membrane
> (peripheral peptide) to see the effect of the peptide on the membrane. I
> want to check the membrane parameters with cpptraj but I cannot find proper
> scripts in the manual for my analysis such as:
>
> - Protein-membrane interaction analysis
>
> - Volume per lipid
>
> - Lateral diffusion of lipids
>
> - Membrane curvature during of protein interaction
>
> - Membrane thickness and its changes during simulation
>
> I would appreciate if somebody could help me in this issue.
>
> Best regards.
>
>
> P.S. similar analyses have been done in the following article but they did
> not mention about the scripts they used.
>
> Skjevik ?A, Madej BD, Dickson CJ, Teigen K, Walker RC, Gould IR. All-atom
> lipid bilayer self-assembly with the AMBER and CHARMM lipid force fields.
> Chem Commun (Camb). 2015;51(21):4402-5.
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 18 Feb 2019 10:34:22 +0100
> From: James Starlight <jmsstarlight.gmail.com>
> Subject: [AMBER] Speed-up calculation of Entropy with MMPBSA
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAALQopxn0wW21BwvpF=Z2iTFoa1p0yYoWQ_UGc5iiR6V0rreEw.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear Amber users,
>
> I am performing MMGBSA post-processing of Amber trajectory for water
> soluble protein of ~ 200 residues bound to sugar ligand. For the 100
> ns trajectory, I take only 200 snapshots, e.g:
> &general
> startframe= 1, interval=5, entropy=1, keep_files=2,
> strip_mask=:WAT:Cl-:NA+:K+, netcdf=1
> /
> &gb
> igb=5, saltcon=0.150,
> /
>
> or
> &nmode
> nmstartframe=1, nminterval=1, nmode_igb=1, drms=0.05, nmode_istrng=0.15,
> /
> #
>
> Using 8 cpus of the local CPU machine I have very fast calculation of
> enthalpy contribution but on the stage of entrophy calculation (via
> NMA or harmonic approximation) the calculations are stuck. Could you
> suggest me something to improve performance of the calculations? Would
> it be possible to use less interval with NMA for calculations of
> enthropy with NMA?
>
> thanks in advance!
>
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 18 Feb 2019 11:29:31 +0000
> From: mish <smncbr.gmail.com>
> Subject: [AMBER] Umbrella Sampling and WHAM analysis
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAFxStkJEAs_apaW7oJE6werShZFvJzGV4nH3EG=+f5nkbEHC7w.mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello everybody,
>
> I've a question regarding umbrella sampling (US) with distances and further
> analysis with the WHAM program of Alan Grossfield. I ran 1D US simulations
> of two a Tryptophan-small-molecule interaction, where I am pulling them
> away in explicit solvent condition. Input file for a window at 4A distance
> looks like:
> -----------------------------------------------------
> 3ns NPT production for angstrom
> &cntrl
> imin = 0, ntx = 5, irest = 1,
> ntpr = 10000, ntwr = 20000, ntwx = 20000,
> ntf = 2, ntc = 2, cut = 10.0,
> ntb = 2, nstlim = 1500000, dt = 0.002,
> temp0 = 300, ntt = 3,
> gamma_ln = 1.0,
> ntp = 1, pres0 = 1.0, taup = 5.0,
> nmropt = 1, ioutfm=0, iwrap=0
> &end
> &wt
> type='DUMPFREQ', istep1=1000,
> &end
> &wt
> type='END',
> &end
> DISANG=dist_04.0
> DUMPAVE=dist_04.0.dat
>
> -------------dist_04.0----------------------------------------------------
> &rst
> iat=-1,-1
> igr1=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19
> igr2=25,27,28,34,38,42
> r1=1, r2=04.0, r3=04.0, r4=17,
> rk2=1.0, rk3=1.0,
> &end
> -----------------
>
> Then I am using WHAM to get PMF
> wham 1 17 50 0.00000001 300 0 wham.in wham.out 10 9999
> where wham.in file has entries for each 13 windows:
> win-03.0/dist01_03.0.dat 3.00 2.00
> ...
> win-15.0/dist01_15.0.dat 15.00 2.00
>
>
> Histograms looks perfectly fine, but the PMF shows me a strange decrease
> after 8A while being pulled away further. I used a TIP4PEWBOX extending 30A
> from the solute to make sure that solute going of of the box is not causing
> any problem. I have tried many more replicas and longer simulations to
> ensure sampling but results are same as here.
>
> I have no clue why PMF starts decreasing while two molecules are separated
> by 8A and there is nothing else to interact other than water molecules.
> There are several -OH in small-molecule but I believe they should have a
> minima while interacting to each other. I am including histogram (upper
> panel) and PMF (lower) from the simulation.
>
> Can someone point-out the possible cause of such a behavior?
> [image: image.png]
> Regards,
> Mish
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 6
> Date: Mon, 18 Feb 2019 07:50:12 -0500
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] Speed-up calculation of Entropy with MMPBSA
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20190218125012.i56xrfzq7obgw4v5.godel.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
> On Mon, Feb 18, 2019, James Starlight wrote:
>
>> I have very fast calculation of
>> enthalpy contribution but on the stage of entrophy calculation (via
>> NMA or harmonic approximation) the calculations are stuck. Could you
>> suggest me something to improve performance of the calculations? Would
>> it be possible to use less interval with NMA for calculations of
>> enthropy with NMA?
>
> Yes: that is a common approximation. Start with fewer snapshots, and
> see how much a computed entropy varies among them. That will give you
> an idea of how many samples you will need to get a good estimate of the
> mean. Generally, the "instantaneous" entropy varies less than does the
> enthalpy.
>
> ....dac
>
>
>
>
> ------------------------------
>
> Message: 7
> Date: Mon, 18 Feb 2019 07:51:58 -0500
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] making force fields files from topology
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20190218125158.yl5kr7xqu7tl2isi.godel.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
> On Thu, Feb 14, 2019, Hadi Rahmaninejad wrote:
>
>>
>> We know that we can easily create topology and coordinate from forcefields
>> files (frcmod and prep files) using tleap or xleap. But, in my case, I have
>> topology and coordinate files of system getting from "Parmed", and need to
>> obtain forcefield files (to change the solvation). Is there any possibility
>> to get forcefield files from topology and coordinate files of system in
>> amber?
>
> Check out the "writeFrcmod" action in parmed, e.g. type "help
> writeFrcmod".
>
> ...dac
>
>
>
>
> ------------------------------
>
> Message: 8
> Date: Mon, 18 Feb 2019 07:55:49 -0500
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] MMPBSA
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20190218125549.cdxgrt6slxdqsadi.godel.rutgers.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> On Thu, Feb 14, 2019, Nisha Amarnath Jonniya wrote:
>>
>> I would like to know that Is it ?Gibbs free energy? or would it be
>> ?Standard Gibbs Free Energy?? which we calculate via MMPBSA scheme.They
>> have different significance. Accordingly, the appropriate notation of G,
>> i.e. G or G(zero) must be used for our equations while mentioning.
>
> The estimates are indeed of standard free energies. Note that all the
> concentration dependence comes in the entropy term (assuming you have a
> reaction with different numbers of molecules for reactants and
> products), so be sure to include that part of the calculation.
>
> ....dac
>
>
>
>
> ------------------------------
>
> Message: 9
> Date: Mon, 18 Feb 2019 13:57:17 +0100
> From: Hosein Geraili Daronkola <geraili.hsn.gmail.com>
> Subject: [AMBER] MBAR from TI on pmemd
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAMQCa1kiSy9q=KwUbrpxDqXYGFg7Sj7JUNB=NSeY+H3oqi3GKQ.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
> I am running TI with Amber18 on GPU.
> I wanted to know how can I use the MBAR data in my output to calculate the
> entropy and enthalpy like a normal MBAR??? I mean, is there any script in
> AmberTools to do that, or outside AmberTools??
> Best
>
>
>
>
> [image: Mailtrack]
> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&>
> Sender
> notified by
> Mailtrack
> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&>
> 02/18/19,
> 1:56:55 PM
>
>
> ------------------------------
>
> Message: 10
> Date: Mon, 18 Feb 2019 08:07:45 -0500
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] Amber18 TI on K10 - any known problem?
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20190218130745.yt5zvc4hrzd5tqbj.godel.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
> On Wed, Feb 13, 2019, Thomas Fox wrote:
>>
>> Im having problems running TI calculations on old K10 GPUs. About 10% of my
>> jobs produce after a while NaNs in the output. Before that, the run looks
>> pretty normal. The bombs are not reproducible, when I run the same set of
>> ligand perturbations multiple times, its always different perturbations and
>> different lambda values that fails. The same systems ran fine multiple times
>> with Amber16.
>
> I'm a little confused here: in Amber16, we did not support TI in
> pmemd.cuda. Can you say more about what you ran with Amber16?
>
>>
>> My setup: Amber18, with all updates installed, RH SL6.8 with Cuda8.0. TI
>> with softcoremasks, with/without HMR. I only observe the crashes on
>> K10.G1.8GB or K10.G2.8GB, runs on K40m or K40c or GTX1080 cards seem to be
>> fine.
>
> This might be a bit hard to track down, since (at least here) we don't
> have easy access to K10 cards. Maybe someone on the list can try to
> volunteer to reproduce the problem (if you have files that you can
> share). I don't remember seeing any reports of K10-specific problems,
> but I'm guessing very little testing was ever done: even back at
> Amber12, only K20's or higher numbers were tested.
>
>>
>> Any idea how I could trace the source of the problem? Any known issues I
>> should be aware of - e.g. some weird combination of input parameters that I
>> use? For reference, I have attached my mdin file (and please no flames - I
>> know that my input parameters do not reflect the current state of the art -
>> but hints for improvement are certainly welcome :-).
>
> Depending on the system, dt=0.004 for a softcore TI run is pretty
> aggressive. Also, you should definitely set vlimit=20. (or similar
> value), which will damp occasional giant velocity jumps. If you have
> the time, might be worth a check using vlimit and a shorter time
> step (or both).
>
> ...dac
>
>
>
>
> ------------------------------
>
> Message: 11
> Date: Mon, 18 Feb 2019 08:09:00 -0500
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] Interpreting QM MMPBSA results
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20190218130900.hhickw7o42nenk3t.godel.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
> On Tue, Feb 12, 2019, Sundar wrote:
>
>> Following is my input file for QM-MM-GBSA calculations.
>> The DELTA Total in the output file is "nan".
>> MM-GBSA works fine though. The error is only when I try QM.
>
> Look at the outputs for the individual frames. Check for things like
> SCF convergence problems. If this only happens on some frames, you may
> need to filter out those manually.
>
> ...dac
>
>
>
>
> ------------------------------
>
> Message: 12
> Date: Mon, 18 Feb 2019 14:16:41 +0100
> From: James Starlight <jmsstarlight.gmail.com>
> Subject: Re: [AMBER] Speed-up calculation of Entropy with MMPBSA
> To: david.case.rutgers.edu, AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAALQopz+rCwcAnDe1K_4Tdvjr9NWE-R09t+DMKDATfJ2b4S6gQ.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Thanks for the idea!
> Does the harmonic approximation generally faster compared to NMA
> assuming same number of given snapshots?
>
>
> ??, 18 ????. 2019 ?. ? 13:50, David A Case <david.case.rutgers.edu>:
>>
>> On Mon, Feb 18, 2019, James Starlight wrote:
>>
>>> I have very fast calculation of
>>> enthalpy contribution but on the stage of entrophy calculation (via
>>> NMA or harmonic approximation) the calculations are stuck. Could you
>>> suggest me something to improve performance of the calculations? Would
>>> it be possible to use less interval with NMA for calculations of
>>> enthropy with NMA?
>>
>> Yes: that is a common approximation. Start with fewer snapshots, and
>> see how much a computed entropy varies among them. That will give you
>> an idea of how many samples you will need to get a good estimate of the
>> mean. Generally, the "instantaneous" entropy varies less than does the
>> enthalpy.
>>
>> ....dac
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 13
> Date: Mon, 18 Feb 2019 19:12:04 +0530
> From: Nisha Amarnath Jonniya <phd1601271002.iiti.ac.in>
> Subject: Re: [AMBER] MMPBSA
> To: david.case.rutgers.edu, AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CACrpWRdLZRGwSi-+6O7CiNgy1-cqA8Mptb3s_8X7ve98LzNMWw.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Thank you.
>
> On Mon, 18 Feb 2019, 7:07 pm David A Case <david.case.rutgers.edu wrote:
>
>> On Thu, Feb 14, 2019, Nisha Amarnath Jonniya wrote:
>>>
>>> I would like to know that Is it ?Gibbs free energy? or would it be
>>> ?Standard Gibbs Free Energy?? which we calculate via MMPBSA scheme.They
>>> have different significance. Accordingly, the appropriate notation of G,
>>> i.e. G or G(zero) must be used for our equations while mentioning.
>>
>> The estimates are indeed of standard free energies. Note that all the
>> concentration dependence comes in the entropy term (assuming you have a
>> reaction with different numbers of molecules for reactants and
>> products), so be sure to include that part of the calculation.
>>
>> ....dac
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> ------------------------------
>
> Message: 14
> Date: Mon, 18 Feb 2019 12:13:22 -0500
> From: Hadi Rahmaninejad <ha.rahmaani.gmail.com>
> Subject: [AMBER] ChamberParm objects are not supported by this action
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CABZiX_RWe7EyYQuM2XLYN0D0TdMAV8w0C68Sr4+xNV-Fxj6kJg.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hello Amber Users
>
> I am trying to create forcefield files from topology and coordinate file I
> got using "Parmed" and "chamber" command. The method I am using is by
> "writeFrcmod" command, which was recommended from another amber user here
> in mailing list. However, I am getting this error message: "ChamberParm
> objects are not supported by this action". I suspect if the reason is
> inorganic atom (Si) that I am using, but I am not sure. I appreciate if
> anyone can help me with this.
>
> Thank you,
> Hadi
>
>
> ------------------------------
>
> Message: 15
> Date: Mon, 18 Feb 2019 18:54:13 +0100
> From: "MYRIAN TORRES RICO" <myriam.torres.iiq.csic.es>
> Subject: [AMBER] puckering coordinates
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <20190218185413.Horde.QHj6i1cUZxCcVFfOVE5aESG.webmail.csic.es>
> Content-Type: text/plain; charset=utf-8; format=flowed; DelSp=Yes
>
> Hi all,
>
> I have a complex protein-saccharide and I want to calculate the
> puckering coordinates (q,f) in the six ring. How is the scrypt?
>
> thanx in advantage
>
> Myriam
>
>
>
>
> ------------------------------
>
> Message: 16
> Date: Mon, 18 Feb 2019 14:21:07 -0500
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] ChamberParm objects are not supported by this
> action
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20190218192107.fkbfmdxxpja75zhj.godel.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
> On Mon, Feb 18, 2019, Hadi Rahmaninejad wrote:
>>
>> I am trying to create forcefield files from topology and coordinate file I
>> got using "Parmed" and "chamber" command. The method I am using is by
>> "writeFrcmod" command, which was recommended from another amber user here
>> in mailing list. However, I am getting this error message: "ChamberParm
>> objects are not supported by this action". I suspect if the reason is
>> inorganic atom (Si) that I am using, but I am not sure. I appreciate if
>> anyone can help me with this.
>
> OK...my apologies: I failed to realize the limitations of the
> writeFrcmod action. My guess(!) is that the problem is not Si per se,
> but is rather related to the fact that CHARMM force fields are supported
> in a somewhat convoluted way in Amber, that cannot be back-ported to a
> frcmod file.
>
> Stated another way: the chamber conversion is done via a low-level
> (prmtop) manipulation, and there is no (current) way to translate this
> back to a high-level (frcmod) file format. I suspect you may have to
> re-build the system (say with a new solvent) in CHARMM, then re-run
> parmed/chamber to get the updated Amber prmtop file.
>
> Amber users that know more than I do should chime in here!
>
> ....dac
>
>
>
>
> ------------------------------
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> End of AMBER Digest, Vol 2562, Issue 1
> **************************************
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Received on Mon Feb 18 2019 - 12:30:03 PST
