Contributors

S. Pendley, T. E. Cheatham III
Departments of Pharmaceutics and Pharmaceutical Chemistry
University of Utah

References

S. Pendley, T. E. Cheatham III
Molecular dynamics guided study of salt bridge length dependence in both fluorinated and non-fluorinated parallel dimeric coiled-coils
Scott S. Pendley, Yihua B. Yu, Thomas E. Cheatham III
Proteins: Structure, Function and Bioinformatics 2008, 74, 612

Comments

hep.off = Heptanoic Acid
tfl.off = 5,5,5-trifluoroleucine
hfl.off = 5,5,5,5',5',5'-hexafluoroleucine
nor.off = N-terminal Ornithine
orn.off = Ornithine

No frcmod file supplied because no new parameters (besides the charges) required. Capping groups of ACE and NME were used to create the dipeptide consistent with the Cornel et al forcefields. Charges were determined using a 2 stage method, I used Gaussian 98 (HF 6-31g*) to minimize the structure using tight convergence and an SCF criterion of 10^-8 au. Gamess (HF 6-31g*) was used to calculate the MEP using six different orientations. RESP converted the MEP to resp charges averaged along the different orientations and accurate to six digits beyond the decimal point.

Regarding Heptanoic Acid: Full complete name is (S)-2,7-Diaminoheptanoic acid
References:
"Preparation and Microbiological Activity of an Homolog of Lysine", JACS 1951 McLaren and Knight
"DL-4-Oxalysine, an Inhibitory Analog of Lysine", JACS 1957 McCord, Skinner, Shive

[ APD Home ] [ Submit Parameters ] [ Amber Home ] [ UK Mirror ] [ Pharmacy Home ] [ Contact ]
Last modified Fri Jul 14 18:15:00 BST 2006