AMBER Archive (2008)

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

From: Waqas Nasir (nasirwaqas1983_at_yahoo.com)
Date: Thu Sep 04 2008 - 09:12:21 CDT

Hi,

Well, I have tried straight single point md on the complex,sugar and protein separately, and what I have found is as follows;

For the complex;

--------------------------------------------------------------------------------
 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 360.57 PRESS = 0.0
 Etot = -11596.6095 EKtot = 8487.1166 EPtot = -20083.7261
 BOND = 205.6242 ANGLE = 1549.3183 DIHED = 1658.6775
 1-4 NB = 2829.7862 1-4 EEL = 25430.2124 VDWAALS = -3397.0162
 EELEC = -41653.4404 EGB = -6819.9179 RESTRAINT = 0.0000
 ESURF= 113.0299
 ------------------------------------------------------------------------------

For the protein subunit;

--------------------------------------------------------------------------------
 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 360.54 PRESS = 0.0
 Etot = -6198.6938 EKtot = 8398.2944 EPtot = -14596.9881
 BOND = 1631.1279 ANGLE = 4308.2912 DIHED = 6362.1576
 1-4 NB = 2235.1943 1-4 EEL = 24344.5199 VDWAALS = -5021.8633
 EELEC = -40717.4825 EGB = -7853.7023 RESTRAINT = 0.0000
 ESURF= 114.7691
 ------------------------------------------------------------------------------

And for the sugar subunit;

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

With the following input file used;

&cntrl
  imin = 0,
  ntx = 1,
  irest = 0,
  ntb = 0,
  ntr = 0,
  ntc = 2,
  ntf = 2,
  igb = 2, saltcon = 0.2, gbsa = 1,
  tempi = 300.0,
  temp0 = 300.0,
  ntt = 1,
  tautp = 1.0,
  nstlim = 0, dt = 0.0,
  ntpr = 0, ntwx = 0, ntwr = 0,
  cut = 12
 /

Now this time the results are totally opposite of what we had before... I am brutally murdered by these energy calculations... please if you could help...
Thanks,
Waqas.

----- Original Message ----
From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
To: amber_at_scripps.edu
Sent: Thursday, September 4, 2008 1:39:48 PM
Subject: Re: AMBER: Need help... High energies for complex...

is this the complex after minimization?

I think to clarify things you should compare everything (complex and
separated) without the minimization part. just use the snapshot and
see if they match better. then you can start to work on whether
minimizing changes things.

On Thu, Sep 4, 2008 at 6:08 AM, Waqas Nasir <nasirwaqas1983_at_yahoo.com> wrote:
> 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
>> > ===================================================================
>> > -----------------------------------------------------------------------
>> > The AMBER Mail Reflector
>> > To post, send mail to amber_at_scripps.edu
>> > To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> > to majordomo_at_scripps.edu
>> >
>> >
>>
>>
>>
>> --
>> ===================================================================
>> 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
>> ===================================================================
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber_at_scripps.edu
>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> to majordomo_at_scripps.edu
>
>
>
> --
> Regards,
> Neha Gandhi,
> School of Biomedical Sciences,
> Curtin University of Technology,
> GPO Box U1987 Perth,
> Western Australia 6845
>
> 

-- 
===================================================================
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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