Hi George,
In order to determine the initial distance you have to do a quick
jarzynski simulation. In your mdin set nstlim=11 and set &wt
type='DUMPFREQ', istep1=1. Next open the file which was set equal to
DUMPDAVE (I believe in your case it was "dist_vs_t") and look at column 2
of the first row and that will tell you what value (r2) should be. As far
as how to set (rk2) I have found that a value 400.0 has worked well to me
but you will have to look at your system to determine what the appropriate
should be.
On Tue, Jan 31, 2012 at 12:44 PM, George Tzotzos <gtzotzos.me.com> wrote:
> Hi Dwight
>
> Following your very useful suggestions, I have two additional queries.
>
> 1. Since you selected specific atoms in your receptor mask, what criterion
> did you use to define the initial distance (r2) between the ligand and the
> receptor?
>
> 2. What criterion did you use to define rk2 which I assume is in *
> kcal/mol-A^2* . Isn't the value (=500.0) on the high side?
>
> With thanks
>
>
> George.
>
>
>
>
> On Jan 25, 2012, at 3:06 AM, Dwight McGee wrote:
>
> Hi George,
>
> If you are trying to identify pathways, then it is better to use a center
> of mass restraint like you stated. I have attached an example of how I have
> specified it for my system. The flag "igr1" is the mask for the atoms in
> the receptor, where I only chose "CA" atoms for the mask. I am not sure
> what protein you are performing steered molecular dynamics on, but if there
> are such things as flaps that lie over the active site, then you will not
> want to include those in the "igr1" mask. The flag "igr2" signifies atoms
> belonging to the ligand in which I only included the heavy atoms; the
> hydrogens were not included.
>
> On Tue, Jan 24, 2012 at 8:40 AM, George Tzotzos <gtzotzos.me.com> wrote:
>
> Hi everybody,
>
>
> I'm a complete novice in this and I'm trying to follow the Manual.
>
>
> In summary, I'm trying to identify receptor tunnel(s) through which a
>
> ligand can be released from the binding pocket.
>
>
> I'm using the restraint and input files attached at the end of this
>
> message.
>
>
> As can be seen from the .rst file, I'm changing the restraint between
>
> atoms. I have a feeling that this is wrong. Wouldn't it be better to use
>
> something like a distant restraint between the centre of mass of the
>
> protein and the ligand? If so, how can one define these centres? In this
>
> case, I assume that the iat variable would have to be changed. To what?
>
>
> A second question relates to the directionality of the "push"? Is there
>
> one? Should one repeat the simulation using different atoms within the
>
> binding pocket of the protein?
>
>
> Apologies if these questions are naive but I need to start from somewhere
>
> and I'm not at all familiar with restraints applied in NMR.
>
>
> Thanks in advance for any help
>
>
> George
>
> ======================
>
> dist.RST
>
> # Change distance restraint between atoms
>
> &rst iat=1533,2223, r2=4.492, rk2=14.0, r2a=18.0 /
>
> #1533 (protein atom); 2223 (ligand atom)
>
>
> smd.in
>
> smd 2wc6-bombykol
>
> &cntrl
>
> imin=0,irest=1,ntx=5,
>
> nstlim=1000,dt=0.002,
>
> ntc=2,ntf=2,
>
> cut=8.0, ntb=2, ntp=1, taup=2.0,
>
> ntpr=1, ntwx=1, ntwr=1,
>
> ntt=3, gamma_ln=2.0, ig=-1,
>
> temp0=300.0,
>
> jar=1,
>
> /
>
> &wt TYPE='DUMPFREQ', istep1=1, /
>
> &wt TYPE='END', /
>
> DISANG=dist.RST
>
> DUMPAVE=dist_vs_t
>
> LISTIN=POUT
>
> LISTOUT=POUT
>
>
>
> _______________________________________________
>
> AMBER mailing list
>
> AMBER.ambermd.org
>
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
>
> --
> T. Dwight McGee Jr.
> Quantum Theory Project
> University of Florida
> Graduate Student
> dwight.mcgee.gmail.com
>
> "Problems cannot be solved at the same level of awareness that created
> them."
> Albert Einstein
> <dist.RST.nfv.mut.orig>_______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
--
T. Dwight McGee Jr.
Quantum Theory Project
University of Florida
Graduate Student
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 31 2012 - 11:30:02 PST
