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
>>
>>
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>>
>
>
>
> --
> 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
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Received on Tue Jan 31 2012 - 10:00:02 PST
