Hi Dwight
Many thanks. Indebted. Will try today on the basis of your suggestion
George
Sent from my iPhone
On 25 Jan 2012, at 03:06, Dwight McGee <dwight.mcgee.gmail.com> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jan 25 2012 - 00:00:03 PST
