Summary of information
PROJECT
Deoxyadenosine

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Upload 01-12-2005 14:31 (Day-Month-Year, Paris time)
Update 28-09-2011 09:06 (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

DADE C10H13N5O3 Adenine Deoxyribose Nucleoside


Abstract

RESP atomic charges for Deoxyadenosine (conformations C2'endo and C3'endo) 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. conformations and 12 mol. orientations (Rigid-Body Reorientation Algorithm) for each conformation. Charge values to be compared with those reported in the projects W-65, W-66 and W-67.

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 WHOLE MOLECULE

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 Deoxyadenosine Link Wiki Logo Jmol Logo


Number of molecule(s) used in the charge derivation procedure 1

File(s) provided to the PDB format

No Molecule name Conformation No Reorientation procedure Mol. orientation No Download Wikipedia
1 Deoxyadenosine 2 Rigid Body Reorient Algo 12 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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