Hi Fabricio,
Where exactly are the C16 an C17 atoms in your lipids? I have used the fxyz functionality but using all nitrogen atoms in POPC lipid head groups (on both sides of the membrane, such that the center-of-mass defined by the nitrogens is approximately the middle of the bilayer). Or you could try the phosphorus atoms.
Callum
________________________________
From: Fabrício Bracht <fabracht1.gmail.com>
Sent: Tuesday, October 11, 2016 8:26:15 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Ligand across membrane
Actually, I found the fxyz variable. The problem is that, for example, as I
did, if you define the distance between the COM of the molecule and the
lipid bilayer, you need to choose (max 1024, for pmemd, I think) atoms from
the bilayer that will allow you change the distance, and that this
distances will sample the crossing of the bilayer.
I chose the c16 and c17 carbon atoms, but it did not work as expected. So,
I was thinking if it would be possible to define a plane point distance or
if the reaction coordinate can be defined relative to the box center.
Or if you have any other suggestion, I would like to hear it.
Thank you
Fabrício
Em 11 de out de 2016 6:14 PM, "Charles Lin" <clin92.ucsd.edu> escreveu:
> 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 Wed Oct 12 2016 - 07:00:03 PDT
