AMBER Archive (2008)

Subject: Re: AMBER: Need help... High energies for complex...

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Sep 09 2008 - 08:46:19 CDT

minimizing the 3 files separately will not allow you to see if the
energies are additive. as I've said a few times in this thread, you
MUST have identical coordinates in order to test your prmtops.

On Tue, Sep 9, 2008 at 9:16 AM, Waqas Nasir <nasirwaqas1983_at_yahoo.com> wrote:
> Hi,
>
> Hope you are fine.
>
> Well, yes I separated the 2 subunits first and then minimized all three
> files separately with same input file. I will, hopefully try and get the new
> parameter files for proteins.
>
> "you have to watch out not just for the order of prmtop generation, but
> where you load the frcmod files. I'm not sure if there is any overlap
> between ff99 and glycam, but it's something to keep in mind."
>
> I could not get the complete picture here, do you mean that the order is
> always important and moreover do you have any recommendations about loading
> frcmod files in these protein sugar cases.
>
> Thanks,
> Waqas.
>
> ----- Original Message ----
> From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
> To: amber_at_scripps.edu
> Sent: Monday, September 8, 2008 7:45:51 PM
> Subject: Re: AMBER: Need help... High energies for complex...
>
> please try to be very clear about your procedures- do you mean you
> minimized all 3 systems, or minimized the complex and then directly
> separated the coordinates with no further minimization? these are
> different.
>
> you have to watch out not just for the order of prmtop generation, but
> where you load the frcmod files. I'm not sure if there is any overlap
> between ff99 and glycam, but it's something to keep in mind.
>
> finally, my advice is that you should NOT use ff99 for the protein.
> there has been a lot of discussion on this in the email reflector as
> well as in the literature.
>
>> Secondly, after minimization the DIHED values are a bit distorted, I mean
>> they do not accurately sum up to the complex but are close anyways. But
>> the
>> bond and angle values are accurate.
>> I would appreciate if somebody could comment.
>>
>> Thanks alot for the help that you people provided me with,
>> I really do appreciate that..
>> Thanks once again!
>> Regards,
>> Waqas.
>>
>>
>> ----- Original Message ----
>> From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
>> To: amber_at_scripps.edu
>> Sent: Friday, September 5, 2008 12:07:01 PM
>> Subject: Re: AMBER: Need help... High energies for complex...
>>
>> 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_at_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_at_gmail.com>
>>> To: amber_at_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_at_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_at_gmail.com>
>>>> To: amber_at_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_at_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_at_biomaps.rutgers.edu>
>>>>> To: amber_at_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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>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>> --
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>>
>
>
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