AMBER Archive (2009)

Subject: Re: [AMBER] EPtot for Alpha-L- methyl fucose

From: Sushil Mishra (sushilbioinfo_at_gmail.com)
Date: Fri Jul 10 2009 - 09:12:28 CDT

Thanx for your kind reply. I want to calculate free energy of binding for
protein and alpha-L methyl fucose. I fallowed the same procedure give in
amber tutorial (TUTORIAL
2<http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_two/index.htm>:
Using dynamics simulations to estimate binding energetics. (*Beginner*)). in
the tutorail the are getting binding energy is simply by Ecomplex - Eprotein
- Epeptide. But unfortunately for my case i am getting the free energy of
binging very much different. it is in +ve. I have PDB of my protein and
fucose which i showing -9.5 Kcal/mol free energy of binding in ITC and SPR
experiments.
i an getting
Ecomplex = - 5164
Eprotein = - 5248
Epeptide = + 74

so wat may be problem. paramatre choosen by me was same posted earlier, when
i an chooding INTDIAL from 1 to 4 ..value is changing but binding energy is
not -ve in any case. could you tel me how should i proceed for this ??

sincerely
sushil

On Fri, Jul 10, 2009 at 3:57 PM, Carlos Simmerling <
carlos.simmerling_at_gmail.com> wrote:

> The total energy has no meaning in molecular mechanics calculations. If you
> tell us what you are trying to learn about the molecule we may be able to
> help you figure out how to do it.
>
>
> On Jul 10, 2009, at 9:47 AM, Sushil Mishra <sushilbioinfo_at_gmail.com>
> wrote:
>
> Hi
>> i want to calculate the free energy of binding of alpha - L Methyl Fucose.
>> I
>> tried to carry out it in amber. when i am running the MD of methyl fucuse
>> seperately it returning the energy in positive. I tried to adjust
>> dielectric
>> constant values. Cuold anyone explain me tha how much should be expect
>> energy for Methyl fucose seperately. i am posting here the method used and
>> the avg of 2000 runs obtained.
>>
>> Production MD
>> &cntrl
>> imin=0, irest=1, ntx=5,
>> nstlim=2000,dt=0.001, ntc=1,
>> ntpr=20, ntwx=20,
>> cut=16, ntb=0, igb=1, intdiel=4,
>> ntt=3, gamma_ln=1.0,
>> tempi=300.0, temp0=300.0,
>> /
>>
>>
>> A V E R A G E S O V E R 2000 S T E P S
>>
>>
>> NSTEP = 2000 TIME(PS) = 4.500 TEMP(K) = 289.64 PRESS =
>> 0.0
>> Etot = 59.8704 EKtot = 22.4469 EPtot =
>> 37.4236
>> BOND = 9.2444 ANGLE = 11.5774 DIHED =
>> 1.5039
>> 1-4 NB = 4.2159 1-4 EEL = 43.5038 VDWAALS =
>> -1.1770
>> EELEC = -22.5976 EGB = -8.8472 RESTRAINT =
>> 0.0000
>>
>>
>> please suggest me what the problem and the energy for methyl fucose is
>> positive. how can i over come from it ??
>>
>>
>> AMBER_at_ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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