I think you're looking for the fxyz nmr namelist variable (added in Amber16)?
Charlie
________________________________________
From: Fabrício Bracht [fabracht1.gmail.com]
Sent: Tuesday, October 11, 2016 2:06 PM
To: AMBER Mailing List
Subject: [AMBER] Ligand across membrane
Hi, I would like to know if there is a way to do umbrella sampling
simulations, using nmr restraints, of a ligand going across a lipid
bilayer. I have tried using COM pulling like so:
&rst iat=-1,-1, iresid=0, r1=-100, r2=-4.5, r3=-4.5, r4=100.0, rk2 = 40.,
rk3 = 40., fxyz=0,0,1,
igr1=30,152,314,317,362,446,570,573,618,702,786,910,913,920,1044,1047,1130,1254,1257,1342,1345,1430,1433,1518,1521,1528,1612,1736,1739,1824,1827,1912,1915,2000,2003,2088,2091,2176,2179,2186,2310,2313,2398,2401,2408,2608,2611,2618,2742,2745,2830,2833,2878,2962,3046,3130,3254,3257,3302,3426,3429,3704,3707,3792,3795,3878,4078,4081,4126,4250,4253,4300,4303,4310,4434,4437,4520,4644,4647,4732,4735,13142,13145,13230,13233,13240,13364,13367,13374,13458,13582,13585,13592,13754,13757,13764,13888,13891,13976,13979,14064,14067,14112,14196,14280,14364,14488,14491,14498,14582,14706,14709,14716,14800,14962,14965,14972,15172,15175,15260,15263,15270,15394,15397,15482,15485,15530,15654,15657,15742,15745,15752,15876,15879,15924,16048,16051,16058,16220,16223,16230,16352,16476,16479,16562,16646,16770,16773,16858,16861,16946,16949,17034,17037,17158,17320,17323,17330,17454,17457,17502,17702,17705,17712,17874,17877,17922,18046,18049,18134,18137,18184,18187,
igr2=1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, outxyz=1, /
Where igr1 are all c16 atoms and c17 atoms of the lipids and igr2 is my
ligand. I used only c16 and c17 because of the atom limit in igr. But this
does not seem to work.
On a previous discussion (
http://archive.ambermd.org/201602/0124.html) it
was mentioned something about the center of mass umbrella
restraint allowing the calculation of free energy of transfer profiles to
move across a membrane bilayer.
Is that true, and, if so, how would one do that?
Thanks
Fabrício
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Received on Tue Oct 11 2016 - 14:30:03 PDT
