AMBER Archive (2009)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Jul 10 2009 - 08:57:34 CDT

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 ??
>
> sincerely
> --
> Sushil K Mishra
> Computational Chemistry Laboratory
> National Centre for Biomolecular Research
> ILBIT, Building A4 - 2.12
> Kamenice 5
> 625 00 Brno
> CZECH REPUBLIC
> Tel. +420 549 492 521
> Mob. +420 774 816 044
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