AMBER Archive (2008)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Sep 04 2008 - 11:21:42 CDT

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
>>
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>>
>
>
>
> --
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Associate Professor Phone: (631) 632-1336
> Center for Structural Biology Fax: (631) 632-1555
> CMM Bldg, Room G80
> Stony Brook University E-mail: carlos.simmerling_at_gmail.com
> Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
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-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
===================================================================
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