R.E.DD.B.: code F-7

Upload 13-12-2005 09:24 (Day-Month-Year, Paris time)
Update 28-09-2011 12:30 (Day-Month-Year, Paris time)

Information about the Author (who submitted the project in R.E.DD.B.)

Firstname Francois-Yves

Lastname Dupradeau

Institute UFR de pharmacie, UPJV

City Amiens

Country FRANCE

General information about the Project

Molecule keywords

NAIB

C4H9NO

(+)NH3-terminal fragment of dimethylalanine

Ammonium

Peptide bond

Abstract

RESP atomic charges for the (+)NH3-terminal fragment of dimethylalanine, (+)NH3C(Me)2CO, (charges derived using Methylammonium and N-Acetyl-L-dimethylalanine-N'-methylamide; conformations: phi = -65.11, psi = -30.51 and phi = -179.70, psi = -179.74) based on the Connolly surface algorithm and the HF/6-31G* theory level. Charges suitable for MD simulations using the Cornell et al. AMBER force field (and/or its adaptations). Charges derived using 2 mol. orientations (rigid-body reorientation algorithm, RBRA implemented in the R.E.D. program) for MeNH3(+), and 2 mol. conformations and 4 mol. orientations (RBRA) for each conformation for ACE-AIB-NME. Charge values to be compared with those reported in the projects F-8, F-9 and F-10.

Publication YES

Author(s) F.-Y. Dupradeau, A. Pigache, T. Zaffran, C. Savineau, R. Lelong, N. Grivel, D. Lelong, W. Rosanski and P. Cieplak

Journal Phys. Chem. Chem. Phys.

Year 2010

Volume 12

Page(s) 7821-7839

"Whole molecule" or "Molecule fragment" type project MOLECULE FRAGMENT

Interface R.E.D. used ? YES

Charge derivation procedure

Number of Tripos mol2 file(s) provided by the author(s) 1

Contain charge values & information about molecular topology

No	Name	Download	Wikipedia	3D Display 1	3D Display 2
1	N-terminal charged fragment of alpha-aminoisobutyric acid

Number of molecule(s) used in the charge derivation procedure 2

File(s) provided to the PDB format

No	Molecule name	Conformation No	Reorientation procedure	Mol. orientation No	Download	Wikipedia
1	Methylammonium	1	Rigid Body Reorient Algo	2
2	N-Acetyl-dimethylalanine-N'-methylamide	2	Rigid Body Reorient Algo	4

Information regarding Quantum Calculations

Geometry optimization

Program 1 GAUSSIAN 1998

Theory level 1 HF

More information 1 Opt=VTight

Basis set 1 6-31G*

Molecular electrostatic potential computation

Program 2 GAUSSIAN 1998

Theory level 2 HF

More information 2 IOp(6/33=2) NoSymm

Basis set 2 6-31G*

Algorithm CONNOLLY SURFACE

Information about the charge fit

Program RESP

Number of stage(s) 2

input of stage 1

input of stage 2

Files the author of the project wishes to provide...

A script to convert Tripos mol2 file(s) into LEaP OFF library(ies) (for AMBER)...

A script to convert Tripos mol2 file(s) into RTF or PSF library(ies) (for CHARMM)...

A file to provide new force field parameters compatible with the Tripos mol2 file(s)...

A file (choice made by the author) to provide more information about the project...

Download the whole project...