no, you cannot conclude anything about binding. all you can conclude
is that there is a problem somewhere in your protocol. anything you
calculate with these will not be correct. you might want to try
working with a calculation that does not require editing of the
molecule or new parameters and see if you can get it to work on a
simpler test case. once you have experience with that, then you might
be able to get this more advanced system to work.
On Fri, Sep 5, 2008 at 5:15 AM, Waqas Nasir <nasirwaqas1983.yahoo.com> wrote:
> Hi,
>
> Thanks once again for such a great help.
>
> This time I have used xleap and done every thing with my hand, rather than
> using a script. This time the result that I have got are better but not
> completely correct. I am sorry for the trouble that I am causing...
>
> Here is the single point md for complex;
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 360.57 PRESS =
> 0.0
> Etot = -11596.4113 EKtot = 8487.1166 EPtot =
> -20083.5279
> BOND = 205.6103 ANGLE = 1549.3622 DIHED =
> 1658.6999
> 1-4 NB = 2829.8000 1-4 EEL = 25430.2414 VDWAALS =
> -3397.0994
> EELEC = -41648.8133 EGB = -6824.3588 RESTRAINT =
> 0.0000
> ESURF= 113.0299
>
> For sugars;
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 335.14 PRESS =
> 0.0
> Etot = 242.2702 EKtot = 79.9191 EPtot =
> 162.3511
> BOND = 15.1725 ANGLE = 47.3410 DIHED =
> -27.5845
> 1-4 NB = 26.3282 1-4 EEL = 592.4065 VDWAALS =
> -16.3978
> EELEC = -374.1894 EGB = -104.0077 RESTRAINT =
> 0.0000
> ESURF= 3.2822
>
> For proteins;
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 360.54 PRESS =
> 0.0
> Etot = -8302.0894 EKtot = 8398.2944 EPtot =
> -16700.3838
> BOND = 190.4378 ANGLE = 1485.0230 DIHED =
> 5266.2811
> 1-4 NB = 2803.4718 1-4 EEL = 24837.8348 VDWAALS =
> -3357.5193
> EELEC = -41233.4669 EGB = -6804.6020 RESTRAINT =
> 0.0000
> ESURF= 112.1559
>
> The energies are still ridiculous... but the bond energy is accurately
> additive where as the angles are almost. But the dihedrals are completely
> out. This time I have done every thing with hand so I know that the prmtop
> and inpcrd files are fine. What option can you think of now... to debug...
> should I go back to the way I created the sugars and everything... I just
> want to confirm a couple of things;
>
> 1. Is the protocol legitimate and proper (The way that I am calculating
> single point energy for each frame)?
> 2. Do you still think that there might be some problem in prmtop and inpcrd
> files (looking at the results)?
> 3. Do you think that these results might reflect the improper state of
> binding of ligand and the proteins, I mean can I conclude from these results
> that the sugar in question DOES NOT bind to proteins at all!!! I am running
> a small 200 ps md without restraints on this complex to see if the ligand
> remains in the binding pocket or flies off...
>
> I would really appreciate if you could comment please... I am new to amber
> and had just started to enjoy it until this happened...
>
> Thanks, and extremely sorry for the trouble that I am causing...
> Regards,
> Waqas.
>
> ----- Original Message ----
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> To: amber.scripps.edu
> Sent: Thursday, September 4, 2008 6:21:42 PM
> Subject: Re: AMBER: Need help... High energies for complex...
>
> if the coordinates are identical, and there is no covalent link, then
> the bond/angle/dihedral energies should be additive. in your case they
> are far from that - look at the bonds.. if there are no bonds between
> protein and sugar, how can the bond energies not sum up? the only
> conclusion I can make is that the parameters in the individual prmtop
> files do not match those in the prmtop for the complex, or perhaps you
> are not really using the same protein coordinates for the complex and
> isolated protein, or for complex and isolated sugar. I don't really
> have any way of knowing how that might have happened.
>
> On Thu, Sep 4, 2008 at 12:14 PM, Waqas Nasir <nasirwaqas1983.yahoo.com>
> wrote:
>>
>> The last mail that I sent you it had exactly the same coordinates in the
>> complex and the separate subunits. I just pasted the coordinates from main
>> file in two separate files for protein and sugar subunits.
>>
>> I will re check with the prmtop and crd files but I doubt if there is
>> anything that I could do... its just 3 bond commands and one saveamberparm
>> command. I dont have enough room to debug. And yes there is no covalent
>> linkage between the sugar and protein.
>> Do you think that its dead sure that something is different in top and crd
>> files ???
>> Do you think, moreover, that combine command might have done something
>> wrong... just a thought...
>>
>> Thanks,
>> Waqas.
>>
>> ----- Original Message ----
>> From: Carlos Simmerling <carlos.simmerling.gmail.com>
>> To: amber.scripps.edu
>> Sent: Thursday, September 4, 2008 6:41:38 PM
>> Subject: Re: AMBER: Need help... High energies for complex...
>>
>> are the coordinates you are using for the complex exactly the same as
>> for the protein and sugar alone (the energies you posted earlier)?
>> if not, then you really can't use this to debug your energies. they
>> must be identical (but separate files).
>> if yes, then there is something wrong in the prmtop files and you will
>> need to go through your procedure for generating the separate files
>> and make sure they are the same.
>> all of this assumes no covalent link between sugar and protein.
>>
>> On Thu, Sep 4, 2008 at 11:22 AM, Waqas Nasir <nasirwaqas1983.yahoo.com>
>> wrote:
>>> Hi,
>>>
>>> Well, thanks a lot for the worthed help.
>>>
>>> Let me explain the whole procedure that I have taken up, I have some
>>> doubts
>>> in the way I have separated the files and the first thing that came into
>>> my
>>> mind after these results was exactly that the top files are not
>>> corresponding to what is in the results.
>>>
>>> Anyways, the sugar that I have is a tetra saccharide. I first constructed
>>> the sugar unit in xleap and added 3 bonds which were missing when I
>>> imported the pdb file into the xleap with glycam_06 force field (The
>>> reason
>>> being not able to find the exact residues in the glycam06 force field as
>>> are
>>> in the pdb file). Along side that I had a protein unit from the part of
>>> the
>>> pdb file which contained protein. I combined both units in xleap by
>>> combine
>>> command and then generated the prmtop and inpcrd files for the main
>>> complex
>>> on which I had all the minimization and md runs going on.
>>>
>>> Secondly the script for generating frames generated 250 pdb files
>>> corresponding to the 250 frames that I had in the trajectory. I again
>>> repeated the same procedure using tleap and constructed a sugar subunit
>>> and
>>> a protein subunit for each frame and generated top and crd files
>>> separately
>>> for the two subunits in each frame. These files were then used for
>>> subsequent single point energy calculations.
>>>
>>> Do you see mistakes in principle of the approach that has been taken up
>>> here???
>>>
>>> Awaiting your response,
>>> Thanks a lot,
>>> Waqas.
>>>
>>> ----- Original Message ----
>>> From: David A. Case <case.biomaps.rutgers.edu>
>>> To: amber.scripps.edu
>>> Sent: Thursday, September 4, 2008 5:36:37 PM
>>> Subject: Re: AMBER: Need help... High energies for complex...
>>>
>>> On Thu, Sep 04, 2008, Waqas Nasir wrote:
>>>>
>>>> Well, I have tried straight single point md on the complex,sugar and
>>>> protein
>>>> separately, and what I have found is as follows;
>>>
>>> This is not what you should do, at least until you understand what is
>>> going on. My suggestion (and Carlos'):
>>>
>>> Make a single prmtop file for the complex. Use this prmtop file for
>>> a single point calculation with two sets of coordinates: one with the
>>> ligand
>>> (sugar) in its binding location, and a second set of coordinates where
>>> you
>>> manually move the ligand to someplace distant from the protein, (but keep
>>> the
>>> protein coordinates identical to what they were in the complex.
>>>
>>> Once you see and understand how that works, you will be ready to try and
>>> interpret other experiments.
>>>
>>> ...regards...dac
>>>
>>> -----------------------------------------------------------------------
>>> The AMBER Mail Reflector
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>>> to majordomo.scripps.edu
>>>
>>>
>>
>>
>>
>> --
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Received on Sun Sep 07 2008 - 06:07:44 PDT
