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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Received on Thu Dec 22 2016 - 03:00:02 PST
