Dear Amber users,
Is there a way I could perform TI energy decomposition as postprocessing, i.e. after I have completed an MD run? Also, is there a way to perform atom- or group-wise (e.g., -OH, =CO, etc.) decomposition, not just per-residue/backbone/side-chain decomposition?
Thanks for your help Dwight.
Sincerely,
Stefan Ivanov
________________________________________
From: Dwight McGee [dwight.mcgee.gmail.com]
Sent: Thursday, December 22, 2016 2:44 PM
To: AMBER Mailing List
Subject: Re: [AMBER] How to perform energy decomposition in Thermodynamic integration with Sander in Amber 14?
Hi Stef,
For examples of how to format your mdin, take a look at some of the test
cases in $AMBERHOME/test/ti_decomp.
Best,
Dwight
On Thu, Dec 22, 2016 at 5:55 AM, Stefan Ivanov <
stefan.ivanov.postgrad.manchester.ac.uk> wrote:
> Dear Amber community,
>
> I am unsure what the proper way to perform per-residue decomposition
> analysis with TI using Sander in Amber 14 is. I have looked through the
> manual and online posts, mostly in the mailing list archive, but have found
> the information insufficient to get it to work.
>
> Say I have a complex between a 137 residue protein with a ligand and 8000
> water molecules + ions.
>
> For running TI with a lambda values of 0.1, I have an input file such as:
>
> &cntrl
> imin = 0, nstlim = 1000000, irest = 1, ntx = 5, dt = 0.001, cut = 8.0,
> ntt = 3, temp0 = 300.0, gamma_ln = 2.0, ig = -1,
> ntc = 1, ntf = 1,
> ntb = 2,
> ntp = 1, pres0 = 1.0, taup = 2.0,
> ioutfm = 1, iwrap = 1,
> ntwe = 10, ntwx = 10, ntpr = 10, ntwr = 10,
>
> icfe = 1, clambda = 0.1, scalpha = 0.5, scbeta = 12.0,
> ifmbar = 1, bar_intervall = 1000, bar_l_min = 0.05, bar_l_max = 0.95,
> logdvdl=1,
> bar_l_incr = 0.05,
> ifsc=1,
> crgmask='',
> scmask=':N33.C1,C2,C3,C4,C5,C6,C7,C8,C9,C10,N1,O1,H1,H2,
> H3,H4,H5,H6,H7,H8,H9',
> /
>
>
> To enable energy decomposition, I would need to add idecomp = 1 (or 2) in
> the control list. The manual says I would also need to add the RRES card in
> the input file but I can't find an example of what the exact formating is.
> The manual itself isn't too descriptive. I would also need no add the RRES
> card in the corresponding input file for the partner complex, correct? Is
> there a way to do backbone/sidechain decomposition or maybe even
> finer-grained decomposition?
>
> Any help would be immensely appreciated.
>
> Best wishes,
>
> Stef
>
>
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>
--
T. Dwight McGee Jr.
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
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Received on Fri Dec 23 2016 - 08:30:02 PST
