Summary of information
PROJECT
N-terminal charged fragment of alpha-aminoisobutyric acid

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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 visualization
1 N-terminal charged fragment of alpha-aminoisobutyric acid Link Wiki Logo Jmol Logo


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 Link Wiki Logo
2 N-Acetyl-dimethylalanine-N'-methylamide 2 Rigid Body Reorient Algo 4 Link Wiki Logo



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 Link

input of stage 2 Link



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

A script to convert Tripos mol2 file(s) into LEaP OFF library(ies) (for AMBER)...Link
A script to convert Tripos mol2 file(s) into RTF or PSF library(ies) (for CHARMM)...Link
A file to provide new force field parameters compatible with the Tripos mol2 file(s)...Link
A file (choice made by the author) to provide more information about the project...Link
A file (choice made by the author) to provide more information about the project...Link

Download the whole project... Link



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