Amber Archive Dec 2003 by subject
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- AMBER: a simple question about HBond energy...
- AMBER: about H-bond definition for TIP3P
- AMBER: About Temperature Regulation
- AMBER: adding extra salt
- AMBER: Amber - compiler help
- AMBER: ambpdb
- AMBER: ANAL/MMPBSA
- AMBER: Antechamber & Ptraj/Rdparm
- AMBER: Antechamber:charges missing
- AMBER: Basic potential question:
- AMBER: basic questions
- AMBER: Carbohydrate connectivity
- AMBER: Compiling on Suse 9 Pro with ifc...
- AMBER: Constant temperature
- AMBER: Curves parameters UU and PP
- AMBER: Energy map
- AMBER: Ewald in Amber 7
- AMBER: gaff atom types for phosphor compouds
- AMBER: GBSA problem
- AMBER: GIBBS - PMF question: How to get <dV/d_lam> during TI calculations?
- AMBER: GIBBS - PMFquestion
- AMBER: Heme and Zn parameters
- AMBER: how to calculate vibration frequency?
- AMBER: How to use quasih?
- AMBER: HT vs no HT
- AMBER: Ibelly and Ewald error message when ewald should be off
- AMBER: initial structures
- AMBER: initial velocity
- AMBER: length of deltaG calcs
- AMBER: lifetime in ptraj hbond
- AMBER: MD
- AMBER: MD: restrt
- AMBER: Message removed at request of author
- AMBER: Mg2+ parameters for RNA usage
- AMBER: minimization on sander
- AMBER: missing of VdW Parameters for N3
- AMBER: MM-PBSA question
- AMBER: MOPAC from antechamber
- AMBER: MSE
- AMBER: MSMS
- AMBER: NAD+ and NADH amber parameters
- AMBER: Nitrated Tyr
- AMBER: Nmode analysis ptn-ligand complex
- AMBER: nmode statistics
- AMBER: nmode, trajectory
- AMBER: no "Input orientation" in g98 log
- AMBER: NO2-TYR
- AMBER: non-zero 10-12 coefficient
- AMBER: order parameter
- AMBER: Paramters for beta and gamma peptides
- AMBER: parmscan
- AMBER: partial charge
- AMBER: PMEMD Performance on Beowulf systems
- AMBER: PMEMD Performance on IBM SP
- AMBER: problems with pressure control
- AMBER: Pseudouridine force field parameters
- AMBER: Ptraj-HBOND
- AMBER: question about namelist
- AMBER: RESP charge redistribution
- AMBER: RESP charges
- AMBER: Resp Esp charge Derive (RED v-1.0) release
- AMBER: roar topology and coordinate files
- AMBER: Sander / Anal
- AMBER: sander output
- AMBER: segmentation fault
- AMBER: Small problems
- AMBER: special gaff atom types available?
- AMBER: Temperature dependent properties of TIP4P and TIP5P
- AMBER: TFE solvent box
- AMBER: The lost velocities in the restart file generated by Ptraj
- AMBER: The restart file generated by Ptraj
- AMBER: Toolchest
- AMBER: umbrella sampling with AMBER
- AMBER: using sander without SHAKE
- AMBER: Vibration frequency of nucleobases
- AMBER: vlimit?
- AMBER: water neighborhood of amide hydrogens
- AMBER: xleap-N/C terminus
- initial structures
- Nmode problem
- Last message date: Wed Jan 14 2004 - 15:53:13 PST
- Archived on: Wed Jan 29 2025 - 05:53:19 PST
