Table of Contents

Knowledge is invariably a matter of degree: you cannot put your finger upon even the simplest datum and say this we know. T.S.Eliot


georgoulia 2009/01/22

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Peptides, the Empirical Approach . . .



Synopsis of Simulations
Sim1 Sim2 Sim3 Sim4
AAAAA extended 80ns
RGWGE extended 200ns
RWMDF helical 24ns extended 40ns extended 130ns extended 166ns
RWTDQ helical 125ns extended 111ns extended 128ns extended 14fast 200ns
RWTDR extended 134ns
RWTWR extended 125ns
RWSRY extended 139ns extended 99ns helical 160ns
EDWRV extended 100ns extended 200ns
RWSDH extended 200ns
RWSDHd extended 200ns
RWSDM extended 200ns
RWSDN extended 200ns
RWSDT extended 200ns
RWSDY extended 200ns
RWQDY extended 113ns
RWQRD extended 200ns
RWPRE extended 72ns
RWQRE extended 63ns
RWRDY extended 200ns
RWRDQ extended 73ns
RWQDQ extended 54ns
RYTDQ extended 50ns
RDGDR extended 100ns
RDWDR extended 22ns
SRWSR extended 60ns
TRDWN extended 90ns
TYKDN extended 90ns
DEDWQ extended 64ns
DPVKW extended 47ns
KQSWE extended 65ns
KWRIE extended 72ns
QPEWD extended 72ns
RTWPQ extended 74ns
WPQSR extended 72ns

Peptides, the Systematic Approach . . .



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Tips & HowTos . . .



* Insert Code to Word



* Calculation of the contribution of interaction terms to folding



* Using the AMBER forcefield
* New systematic.pl script adapted to the AMBER forcefield



* Convert prmtop files to psf files



* Basics of NMR