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 - 09:35:02 CDT

typo - the dihedral sum should be
1658 = 6262 + (-27)
it's still wrong.

On Thu, Sep 4, 2008 at 10:33 AM, Carlos Simmerling
<carlos.simmerling_at_gmail.com> wrote:
> these don't add up for the things that should be additive, like dihedrals.
> 1658 should be equal to 6362+162 (which is obviously is not).
> by guess is that the prmtop files don't really correspond to the
> separated units, or perhaps you're doing something wrong in separating
> the coordinates.
> check your leap scripts that you used to make the prmtop files and
> make sure everything is consistent.
>
> On Thu, Sep 4, 2008 at 10:12 AM, Waqas Nasir <nasirwaqas1983_at_yahoo.com> wrote:
>> 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
>> ===================================================================
>> -----------------------------------------------------------------------
>> 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
> ===================================================================
> 

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