# Re: [AMBER] Potential Energy is positve for a normal ligand

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Mon, 4 Aug 2014 10:53:34 -0400

absolute values of molecular mechanics energies really don't have any
meaning, and zero is arbitrary. the force fields are usually trained to
reproduce energy differences between different conformations, or
derivatives (forces) for MD. In both cases there is a constant that cancels.

On Mon, Aug 4, 2014 at 10:49 AM, Sun <sunbintyy.163.com> wrote:

> Dear all,
> I have a simple rigid ligand whoes structure is simple ( PDB format
> structure is given below), and I want to calculate itâ€™s potential energy in
> gas phase by using the AMBER GAFF force field, I minimized the structure by
> using sander in AMBERv11, but when I checked the output file of the
> minimization, I found that the value of the potential energy (EPtot term )
> of the ligand is positve. This finding confused me since in my opinion, for
> a stable ligand, it's potential energy should be a negative value.
> The parameter preparation of the ligand was accomplished by using the
> follwing commands:
> antechamber -i lig.pdb -fi pdb -o lig.prep -fo prepi -c bcc
> parmchk -i lig.prep -f prepi -o lig.frcmod
>
>
> To preclude the unprecise possibility of bcc charge, I regenerate the
> parameter file by using the RESP charge ( the electrostatic potential was
> calculated after an optimization of the ligand performed at HF/6-31G* level
> by using Gaussian), however, with the new RESP charge, the final potential
> energy was still a positive value.
>
> Is the emergence of a positive potential energy normal? If not, what
> possible reasons in my calculation could lead to such a wrong result ?
>
>
>
>
>
>
> HETATM 1 C 1 -6.564 0.702 -0.153
> C
> HETATM 2 C 1 -6.607 -0.647 -0.165
> C
> HETATM 3 C 1 -5.435 -1.336 -0.173
> C
> HETATM 4 C 1 -4.220 -0.693 -0.173
> C
> HETATM 5 C 1 -4.239 0.659 -0.173
> C
> HETATM 6 C 1 -5.395 1.341 -0.164
> C
> HETATM 7 C 1 -3.014 -1.336 -0.171
> C
> HETATM 8 C 1 -1.848 -0.633 -0.171
> C
> HETATM 9 C 1 -1.919 0.710 -0.181
> C
> HETATM 10 C 1 -3.090 1.350 -0.180
> C
> HETATM 11 C 1 -2.876 -2.681 -0.164
> C
> HETATM 12 C 1 -1.690 -3.303 -0.156
> C
> HETATM 13 C 1 -0.571 -2.577 -0.154
> C
> HETATM 14 C 1 -0.633 -1.236 -0.162
> C
> HETATM 15 O 1 -5.519 2.567 -0.165
> O
> HETATM 16 C 1 -6.888 2.964 -0.175
> C
> HETATM 17 C 1 -7.716 1.666 -0.121
> C
> HETATM 18 C 1 -8.565 1.555 1.150
> C
> HETATM 19 C 1 0.724 -0.548 -0.153
> C
> HETATM 20 O 1 -7.702 -1.174 -0.167
> O
> HETATM 21 O 1 -5.580 -2.539 -0.181
> O
> HETATM 22 H 1 -1.037 1.364 -0.187
> H
> HETATM 23 H 1 -3.071 2.453 -0.184
> H
> HETATM 24 H 1 -3.705 -3.396 -0.162
> H
> HETATM 25 H 1 -1.628 -4.405 -0.148
> H
> HETATM 26 H 1 0.402 -3.097 -0.145
> H
> HETATM 27 H 1 -7.099 3.539 -1.108
> H
> HETATM 28 H 1 -7.089 3.632 0.694
> H
> HETATM 29 H 1 -8.344 1.544 -1.035
> H
> HETATM 30 H 1 -9.112 0.587 1.195
> H
> HETATM 31 H 1 -9.326 2.368 1.184
> H
> HETATM 32 H 1 -7.936 1.633 2.067
> H
> HETATM 33 H 1 0.745 0.558 -0.120
> H
> HETATM 34 H 1 1.307 -0.880 0.737
> H
> HETATM 35 H 1 1.296 -0.837 -1.065
> H
>
>
>
>
>
> -Sun
>
>
>
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Received on Mon Aug 04 2014 - 08:00:04 PDT
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