AMBER Archive (2008)

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

From: Waqas Nasir (nasirwaqas1983_at_yahoo.com)
Date: Thu Sep 04 2008 - 05:38:53 CDT

----- Forwarded Message ----
From: Waqas Nasir <nasirwaqas1983_at_yahoo.com>
To: amber_at_scripps.edu
Sent: Thursday, September 4, 2008 12:08:49 PM
Subject: Re: AMBER: Need help... High energies for complex...

Hi,

Well, here is the snapshot of what is happening;

The complex after 110 ps has the following state;

 ------------------------------------------------------------------------------

   KE Trans = 0.6333 KE Rot = 0.3647 C.O.M. Vel = 0.004305

   Translational and rotational motion removed

   KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000

 NSTEP = 50000 TIME(PS) = 110.000 TEMP(K) = 301.05 PRESS = 0.0
 Etot = -7479.4207 EKtot = 7086.0852 EPtot = -14565.5059
 BOND = 1667.4928 ANGLE = 4368.2446 DIHED = 2750.7951
 1-4 NB = 2258.1214 1-4 EEL = 24925.2841 VDWAALS = -5072.6293
 EELEC = -41730.2276 EGB = -7313.0633 RESTRAINT = 3464.8770
 ESURF= 115.5992
 EAMBER (non-restraint) = -18030.3829
 ------------------------------------------------------------------------------

The protein frame corresponding to this state, after minimization and single point md gives the following result;

 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 360.54 PRESS = 0.0
 Etot = -12532.4964 EKtot = 8398.2944 EPtot = -20930.7907
 BOND = 299.1003 ANGLE = 1315.6820 DIHED = 5430.8743
 1-4 NB = 1897.7521 1-4 EEL = 24137.4611 VDWAALS = -5414.9492
 EELEC = -41213.3212 EGB = -7495.9348 RESTRAINT = 0.0000
 ESURF= 112.5447

And finally the result for sugar frame is;

 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 335.14 PRESS = 0.0
 Etot = 152.8328 EKtot = 79.9191 EPtot = 72.9137
 BOND = 6.9118 ANGLE = 12.7070 DIHED = -28.8780
 1-4 NB = 17.2280 1-4 EEL = 589.4409 VDWAALS = -25.5086
 EELEC = -395.3658 EGB = -107.0239 RESTRAINT = 0.0000
 ESURF= 3.4021

And almost the same sort of values are there for all the frames. I dont know what should I make up of this result. The energy in sugars is terribly high.
Any thougts to help???

And Carlos, if you could please explain what sort of problem can I have in the protocol or in other words what exactly should be the protocol if not this...

Thanks alot for your continous help,
Awaiting your response,
Regards,
Waqas.

----- Original Message ----
From: Neha Gandhi <n.gandhiau_at_gmail.com>
To: amber_at_scripps.edu
Sent: Wednesday, September 3, 2008 2:41:16 PM
Subject: Re: AMBER: Need help... High energies for complex...

Hi,

Are you using charged carbohydrate such as heparin? Is there any drastic conformational change in receptor-carbohydrate complex? Are you using the coordinates from last snapshot to calculate the energies or you are starting with the initial complex?

Regards,
Neha

2008/9/3 Carlos Simmerling <carlos.simmerling_at_gmail.com>

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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> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.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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-- 
Regards,
Neha Gandhi,
School of Biomedical Sciences,
Curtin University of Technology,
GPO Box U1987 Perth,
Western Australia 6845

      
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