AMBER Archive (2008)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Sep 03 2008 - 07:04:07 CDT

what do you get for energies if you simply separate the complex and do
sing point energy? you need to see if it's a problem in your protocol
for the minimization or if there is something that doesn't match in
the prmtop files. perhaps it's not the same parameters or force field
for the individual units as they have in the complex. I would suggest
using exactly the same procedure, restraints and all, on all parts of
your calculation (complex and separated).

On Wed, Sep 3, 2008 at 7:45 AM, Waqas Nasir <nasirwaqas1983_at_yahoo.com> wrote:
> Yes, it was the same for single point energy calculations and the complex. I
> did it for snapshots both with and without restraints. But results dont seem
> to differ much...
> The main minimization on complex was with restraints on one of the sugar
> rings.
>
> ----- Original Message ----
> From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
> To: amber_at_scripps.edu
> Sent: Wednesday, September 3, 2008 2:27:06 PM
> Subject: Re: AMBER: Need help... High energies for complex...
>
> did you use the same minimization procedure on the complex?
>
> On Wed, Sep 3, 2008 at 7:20 AM, Waqas Nasir <nasirwaqas1983_at_yahoo.com>
> wrote:
>> Hi,
>>
>> Hope every one is doing fine.
>>
>> Well, I have done some manual single point energy calculations on my
>> protein
>> carbohydrate complex using amber version 8. The protein is a dimmer and
>> the
>> sugar is a tetra-saccharide. The values for the binding energy that I am
>> getting are quite high and are in the order of negative 3500-4500 kcal.
>>
>> The script that I have used breaks each of 250 frames in my md run into
>> separate protein and sugar subunits. Minimization of about 500 steps is
>> then
>> performed on each subunit followed by single point md (one with 0 time
>> steps). The energies from sugar and protein md runs for a single frame are
>> added up. The difference of this value is then taken with the actual
>> energy
>> of the complex, that results is ridiculously high values.
>>
>> Just wanted to have some thoughts on what might have gone wrong in these
>> calculations. Or, what steps one might take to improve the results in
>> general.
>>
>> Any sort of check list is highly appreciated.
>>
>> Thanks a lot for reading...
>> Stay blessed!
>>
>> Regards,
>> Waqas.
>>
>>
>>
>
>
>
> --
> ===================================================================
> 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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