Amber Archive Mar 2006 By Subject
- AMBER:
- AMBER: a challenge: a periodic box that cuts through a monomer
- AMBER: about atomic fluctuation & RMSF
- AMBER: about Br- parameters
- AMBER: About statistics results in MMPBSA_DC pair
- AMBER: aligning polymer with Z-axis of periodic box
- AMBER: amber 8 install problem
- AMBER: Amber 8 under Solaris 9 compilation failed
- AMBER: AMBER 8 VS AMBER 7
- AMBER: Amber 9.
- AMBER: AMBER : About the kinetic energy and temperature (GBSA model)
- AMBER: amber8 and gfortran 4.1.0
- AMBER: amber8 error installation
- AMBER: anal: dihedral error
- AMBER: Announcement: Amber 9 is now available
- AMBER: Antechamber calculations
- AMBER: Average pdb
- AMBER: bond parameters for positively charged guanidine group
- AMBER: charge constraints in resp
- AMBER: charge neutralization with GB
- AMBER: chirality.c error in xleap
- AMBER: constant pH simulation
- AMBER: converting .lib files
- AMBER: Cosine content calculation
- AMBER: CPU utilization with Parallel Sander
- AMBER: Different results between serial and parallel runs in AMBER 8
- AMBER: Dimer Image Wrapping
- AMBER: divalent ions
- AMBER: dynamic memory allocation problem in nmode
- AMBER: energy conservation in NVE ensemble (ntt=0, ntb=1)
- AMBER: error while running sander
- AMBER: Ewald and ibelly
- AMBER: failed to save prm and xyz using ff96
- AMBER: faulty ambpdb compilation?
- AMBER: from Wei Zhang: flight information
- AMBER: G95, SGI and Amber8
- AMBER: GAFF + AM1BCC & small-molecule aggregation
- AMBER: generating parameters for the NADH analogue H4NAD
- AMBER: Gromos to Amber
- AMBER: h bond analysis
- AMBER: heating system
- AMBER: hessian calculation
- AMBER: how to calculate the RMSD and B-factor for all atoms of residue
- AMBER: How to develop charge for my deprotonated glycine
- AMBER: How to give the specific pressure parameter for NTP=2
- AMBER: How to patch the configure script (macosx)
- AMBER: Impropers definition
- AMBER: Input conversion error.
- AMBER: install error
- AMBER: installation problem
- AMBER: k-space cutoff with standard Ewald
- AMBER: leap: syntax error when use source command
- AMBER: LES error
- AMBER: MD and MMPBSA
- AMBER: mm-pbsa
- AMBER: MMPBSA
- AMBER: MMPBSA & PBCAL
- AMBER: modeling a non-standard molecule.
- AMBER: N-H and C-H Residual Dipolar Coupling
- AMBER: NADP(H) parameters
- AMBER: negative values of PBSOL and PBCAL in mm_pbsa result
- AMBER: Nmode vs QM Freq Calculation
- AMBER: NTT for production run
- AMBER: nucgen error
- AMBER: OSX 10.4 G4 xlf90 compilation errors
- AMBER: Parmtop file: ANGLE_EQUIL_VALUE actually in radians?
- AMBER: post-processing replica exchange trajectory
- AMBER: Power Mac G5
- AMBER: prep files for L-sugar residues
- AMBER: prepin format
- AMBER: Problem taking the PDB to the Amber coordinates for calculations
- AMBER: Problem with setbox command...
- AMBER: Ptraj & pca
- AMBER: ptraj help - ERROR in readParm: ... failed to find CHARGE
- AMBER: ptraj: hbond analysis
- AMBER: ptraj:hbond question
- AMBER: question about solvatecap commander
- AMBER: question capping helix ends
- AMBER: quistions about pbsa cacultaion
- AMBER: Related to RESTRAINT_WT
- AMBER: replica exchange hangs
- AMBER: rms processing
- AMBER: sander restart problem
- AMBER: Simulating a periodic crystal
- AMBER: Solvating the system with specific number of water molecules...
- AMBER: Suitable water box
- AMBER: temp control
- AMBER: the total energy is not converge as the cutoff increase
- AMBER: transition metals and the parmcal of the antechamber module
- AMBER: Trouble with combining a non-standard residue with a protein of standard residue
- AMBER: united atoms
- AMBER: using MM_PBSA just for binding site, feasible ???
- AMBER: what is unit of the out put of mmpbsa caculation
- AMBER: Which PTRAJ distribution to use?
- AMBER: Xleap 64 bit installation problem
- AMBER: Zoom
- AMBER:molsurf: molsurf.c:1057: is_buried: Assertion `sarg1 >= 0.0' failed
- hi & question
- To dac --AMBER: anal: dihedral error
- Last message date: Sun Apr 02 2006 - 06:10:17 PDT
- Archived on: Wed Mar 17 2010 - 06:00:33 PDT
