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AMBER Archive (2006) - By Subject
4288 messages sorted by: [ author ] [ date ] [ thread ]About this archive
Starting: Sun Jan 01 2006 - 17:31:12 CST
Ending: Sat Dec 30 2006 - 07:20:23 CST
- [Fwd: AMBER: Long line of input]
- [Fwd: AMBER: Problem with impose in lep]
- [UCE]AMBER: (no subject)
- [UCE]AMBER: Temperature not rising enough during simulated annealing
- about compiling errors for Leap
- about the fix_numbering_pdb.csh in Amber Tutorial_eight
- AMBER Tutorial 2 section 6, rmsd calculation: rmsd for residues number?
- Amber8: problem related to antechamber
- AMBER:
- AMBER: $B#F#e(B complex
- AMBER: $B#F#e(B complex$B!!(B(correction)
- AMBER: "atom number exceeds the MAXATOM"
- AMBER: "average" command in ptraj
- AMBER: "NO CONVERGENCE IN SCF CALCULATION" in divcon in Amber9 package
- AMBER: "noimage" option for radial distribution functions
- AMBER: "The system has extended beyond" error message
- AMBER: "vector" command in ptraj
- AMBER: 'lastrst' error for amber8
- AMBER: (Another) Question about using antechamber with G03
- AMBER: (no subject)
- AMBER: .crd file
- AMBER: 0 steps the same as 1 step?
- AMBER: 1-4 interaction in AMBER8
- AMBER: 1st 2 lines of restart files
- AMBER: 2-D free energy surface using WHAM
- AMBER: 2D-topology
- AMBER: 3Dsig: Struct Bioinfo & Comp Biophysics Meeting, 4-5 Aug. Brazil
- AMBER: 7-Methylguanine force field parameters
- AMBER: <kein Betreff>
- AMBER: A BUG report, "ptraj corrplane"
- AMBER: a challenge: a periodic box that cuts through a monomer
- AMBER: A dummy atom on the center of solute molecule
- AMBER: A few problems on the parameterisation of a Glutamine residue
- AMBER: a ligand file
- AMBER: A problem with Amber force field new parameter derivation
- AMBER: A problem with mm_pbsa
- AMBER: a question
- AMBER: a question about "solvateoct" in AMBER 8
- AMBER: A question about Dynamics.
- AMBER: a quetion
- AMBER: A script file for measuring the distance between 2 atoms during MD
- AMBER: ab initio terminology query
- AMBER: about atomic fluctuation & RMSF
- AMBER: about Br- parameters
- AMBER: About Lennard-Jones Parameters
- AMBER: about ligand charge
- AMBER: About mm_pbsa calculation setting up
- AMBER: about mmpbsa
- AMBER: About placing counter ions
- AMBER: About preparing Zn.lib
- AMBER: about restraint format.
- AMBER: about Silica's polarizability
- AMBER: About statistics results in MMPBSA_DC pair
- AMBER: About the Amber trajectories converted to XPLOR ( = DCD) format
- AMBER: About the creation of 1-4 pairs in AMBER program
- AMBER: about the decomposition energies using mm/pbsa
- AMBER: about the execuation of REMD with sander of amber9
- AMBER: about the shake with self-guide LD
- AMBER: about the std of computational alanine scanning
- AMBER: About the unit of the projection onto eigenvectors
- AMBER: About tleap
- AMBER: About WHAM
- AMBER: Absoft Pro Fortran and AMBER 8 on MacOS X 10.4.4
- AMBER: Acetone box
- AMBER: Acetyl CoA
- AMBER: acidifying a water box
- AMBER: ACML and MASS/MASSV for sander and pmemd
- AMBER: ACS Chicago potential symposia and OASYS abstracts
- AMBER: ACTIVE SITE
- AMBER: Addendum: igb=2 and "bad atom type" conflict
- AMBER: adding polar hydrogens
- AMBER: addions default settings.
- AMBER: addition of subroutine in pmemd module
- AMBER: Advice on linux cluster sought
- AMBER: Again SASA
- AMBER: alanine scan (mm/pbsa)
- AMBER: aligning polymer with Z-axis of periodic box
- AMBER: alpha helix preference problem
- AMBER: amber
- AMBER: AMBER - leap - problems with impose command
- AMBER: amber .off file format question
- AMBER: AMBER 7 and cutoff's
- AMBER: AMBER 7 and restrained bonds.
- AMBER: AMBER 8 - dihedral angles when clambda=1
- AMBER: amber 8 install problem
- AMBER: Amber 8 on Rocks 4, Opteron, PGI 6.1
- AMBER: amber 8 problem
- AMBER: Amber 8 QMMM tests fail on AIX
- AMBER: Amber 8 under Solaris 9 compilation failed
- AMBER: AMBER 8 VS AMBER 7
- AMBER: AMBER 8.0 : Octane Implicit Solvent?
- AMBER: Amber 8.0 MM_PBSA Stability : question about methodology
- AMBER: Amber 8.0 no numerical value and offset for the predicted pKa of many titrable residue!!
- AMBER: AMBER 8: Problem with MPI_Finalize
- AMBER: Amber 9 installation issues
- AMBER: amber 9 installation problem
- AMBER: amber 9 intel 9.1 ia64
- AMBER: Amber 9 Leap install error
- AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft
- AMBER: Amber 9, sander imin = 5, -y flag
- AMBER: Amber 9.
- AMBER: AMBER : About the kinetic energy and temperature (GBSA model)
- AMBER: amber atom type -> length of name
- AMBER: amber compilation on Red Hat 8 with MPICH
- AMBER: AMBER complile problem
- AMBER: Amber crashed due to power surge and giving problems..
- AMBER: amber force field
- AMBER: AMBER force field with namd
- AMBER: Amber H-bond print?
- AMBER: Amber Input file from "qout", "resp.dat"
- AMBER: Amber install on RedHat Linux
- AMBER: Amber Installation Help
- AMBER: Amber Installation Help; link woes
- AMBER: AMBER mdcrd file bigger than 2GB
- AMBER: amber memory usage
- AMBER: AMBER minimization vs. Gaussian optimization
- AMBER: Amber minimization with multiple restraints
- AMBER: amber naming conventions for structure files
- AMBER: AMBER parallel run bombs
- AMBER: Amber parallel version
- AMBER: AMBER Tutorial 2 section 6, rmsd calculation: rmsd for residues number?
- AMBER: AMBER Workshops, London UK 26th - 30th June 2006
- AMBER: amber7 compiling error
- AMBER: Amber7-CHARMM22-TRIPOS force fields
- AMBER: AMBER8 - RDF bug
- AMBER: amber8 and gfortran 4.1.0
- AMBER: amber8 bugfix effects
- AMBER: amber8 compiled erro on opteron with 64 bit
- AMBER: amber8 error installation
- AMBER: Amber8 parallel compilation problems on an OSCAR Cluster
- AMBER: Amber8 parallel compilation problems on EM64T system
- AMBER: Amber8.0 predictied pKa problem for a Lysine!
- AMBER: Amber8: how to do Simulated Annealing and Equilibration
- AMBER: Amber8: problem related to antechamber
- AMBER: amber9
- AMBER: Amber9 - openmpi?
- AMBER: AMBER9 compilation error on IBM Cluster
- AMBER: amber9 compilation error on SGI altix
- AMBER: amber9 compilation problems on EM64T xeon system
- AMBER: Amber9 failure to compile parallel on Rocks 4.2.1 system
- AMBER: amber9 hostfile
- AMBER: Amber9 installation error
- AMBER: AMBER9 installation error on Compaq machine.
- AMBER: AMBER9 INSTALLATION problem on O2 sgi system
- AMBER: AMBER9 netcdf trajectory with VMD 1.8.4
- AMBER: Amber9 Parallel compiled with -lam, how to run test.parallel?
- AMBER: amber9 parralel compiling
- AMBER: Amber9 patch bugfix.all issue on SunOS 5.1
- AMBER: amber9 serial compilation error
- AMBER: amber9 serial compile with pathscale on SuSe10.1/AMD64
- AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred
- AMBER: Amber9 test error on SGI Altix
- AMBER: amber9 Test Failer
- AMBER: Amber9 under SGI Prism (Altix) with Intel 8.0 error in pbpgb test
- AMBER: Amber9/mpich2 performance
- AMBER: Amber9: Free Energy
- AMBER: AMBER9: MacG5 parallel sander.MPI
- AMBER: amber9: SA Bomb in sa_arc
- AMBER: Amber: Can't get sander to run
- AMBER: Amber: disufide bond
- AMBER: Amber: Parallel Installation Problems
- AMBER: amber: problem in center command
- AMBER: Amber: Segfault while running sander
- AMBER: ambpdb -pqr
- AMBER: ambpdb and original PDB
- AMBER: AMD 64 Installation / configuration clarification
- AMBER: amidine group/ gaff parameters
- AMBER: ammonia parameters
- AMBER: An issue with the "multimolecule and multiconformational" resp fit
- AMBER: anal vs sander
- AMBER: anal: dihedral error
- AMBER: analysing water behavior during MD
- AMBER: analysis of atoms in a range during simulation
- AMBER: analysis of ATOMs in ´certain range distance during simulation
- AMBER: angle between helices
- AMBER: angle between planes
- AMBER: angle between two vectors
- AMBER: angle between two vectors. .
- AMBER: Angle restraint
- AMBER: ANN: APBS/Amber interface released
- AMBER: Announcement: Amber 9 is now available
- AMBER: Announcement: Parameters for Modified Nucleosides in RNA
- AMBER: Another Installation Problem
- AMBER: another question: is rms 2E-2 good for nmode ntrun=1?
- AMBER: antechamber
- AMBER: Antechamber & atom types
- AMBER: Antechamber - NH2 and C not planar when it should be on one of my ligand
- AMBER: Antechamber 1.26 is released
- AMBER: Antechamber : +ve charge species
- AMBER: antechamber and FMN
- AMBER: Antechamber and gaussian questions
- AMBER: antechamber bond typing questions
- AMBER: Antechamber calculations
- AMBER: antechamber charge calculation very sensitive to conformations ?
- AMBER: antechamber error -> metals
- AMBER: antechamber failure on FMN
- AMBER: antechamber for a database of organic molecules
- AMBER: antechamber help needed for FAD
- AMBER: Antechamber Package Announcement
- AMBER: Antechamber poorly define atom angles of a five ring system which causes NH2 and C not to be planar as expected
- AMBER: antechamber problem
- AMBER: Antechamber RESP charges do not sum to zero even with -nc 0 flag
- AMBER: antechamber:tutorial
- AMBER: antechamber:tutorial. .
- AMBER: Any difference about RESP or ESP with Chelpg or MK
- AMBER: any work-around for 80 character mask string limit?
- AMBER: applying restraints on pre-defined planes
- AMBER: Ask for help in pbsa error in AMBER9
- AMBER: Ask for your help to install Amber8 software
- AMBER: ATCOR.dat format
- AMBER: Atom Exclusion
- AMBER: atom nomination in the PDB file produced by Amber
- AMBER: atom type "O3" not recognized by XLeap
- AMBER: atom type nh vs. n2
- AMBER: Atom Type problem
- AMBER: atome type error
- AMBER: atomifluct
- AMBER: Atoms overlapping
- AMBER: attachments for my last mail
- AMBER: Average pdb
- AMBER: average struct.problem
- AMBER: Backbone & Sidechain atoms: Definition
- AMBER: bad atom type: Li
- AMBER: bad connectivity
- AMBER: bad connectivity - more detail
- AMBER: base-base interaction
- AMBER: basic minimize question
- AMBER: best way to customize linkages
- AMBER: big bond energy change from minimization and md (heating)
- AMBER: binpos file
- AMBER: BioBlade
- AMBER: Biomolecular Simulation 2007
- AMBER: bond command between Zn and a CYM residue in one chain of a protein complex
- AMBER: Bond Force Conctants in Amber Force Fields
- AMBER: bond information
- AMBER: bond information in amber
- AMBER: bond parameters for positively charged guanidine group
- AMBER: bondtype problem
- AMBER: Born igb =2
- AMBER: brookhaven to amber pdb format
- AMBER: bug in ambpdb (AMBER8)
- AMBER: bugfix
- AMBER: bugfix for frcmod.ff03 in Amber 9
- AMBER: bugfix for impropers in parmchk
- AMBER: Bugfixes available for pmemd iwrap problem
- AMBER: build a polymer with sequence command
- AMBER: build box info for acetonitrile in the simulation with periodic boundary condition
- AMBER: building a box
- AMBER: building AMBER9 with gfortran/cygwin
- AMBER: Building an RNA - Proflavin Complex
- AMBER: Building Library
- AMBER: Building Parameters
- AMBER: Building polymer with sequence command
- AMBER: C -N -CT-CT torsion parameters
- AMBER: Ca2+ polarizability
- AMBER: Calculate interaction energy between small organic molecules
- AMBER: calculating box dimensions during MD
- AMBER: calculating dihedral angles, radius of gyration
- AMBER: Calculating energy for specific part of system
- AMBER: Calculating native contacts for mdcrd files
- AMBER: Calculation of Dihedral constants
- AMBER: Calculation of g(r) from PTRAJ
- AMBER: cAMP ligand charge
- AMBER: cAMP ligand file
- AMBER: Can I run RED/RESP for Platinum Complexes?
- AMBER: can i use unusual amino acid
- AMBER: Can salt effect be determined in GB medel?
- AMBER: Can we submit jobs in sequences to amber?
- AMBER: Can we use the distance restraint in Replica-exchange simulation with AMBER8
- AMBER: Can you use VMD to measure bond angles/lengths
- AMBER: Can't compile PMEMD
- AMBER: Can't open xleap
- AMBER: Cannot successfully assign bond type for this molecule?
- AMBER: carnal prob
- AMBER: CARNAL: carnal source code
- AMBER: CARNAL: H-BOND Specifying side chains only
- AMBER: Carnal: Internal error: stream file name 2 out of range
- AMBER: center molecule using iwrap=1?
- AMBER: center of mass dihedral restraints
- AMBER: change atom in a DNA double strand
- AMBER: change from .rst file to .mdcrd file
- AMBER: change mdcrd file to pdb file
- AMBER: charge constraints in resp
- AMBER: Charge fitting in Amber
- AMBER: charge in LEaP step
- AMBER: charge models in antechamber
- AMBER: charge neutralization with GB
- AMBER: Charge of the phosphorylated Ser/Thr in MM_PBSA calculation
- AMBER: charge problem in MM-PBSA
- AMBER: charge redistribution in .prep files
- AMBER: Charges from NMR spin densities
- AMBER: Charges of enantiomers for Amber8
- AMBER: Charges on atoms in protein :AMBER
- AMBER: charmm force field in amber9
- AMBER: check as error: load prepin in tleap
- AMBER: checkmask
- AMBER: checkoverlap doubt [was: Post-MD minimization]
- AMBER: chemical shift restrains
- AMBER: chirality.c error in xleap
- AMBER: chirality.c line 121
- AMBER: Closest(closest water)
- AMBER: cluster architecture for the best amber performance
- AMBER: COM
- AMBER: Combine amber-force field and gaff94 for one molecule?
- AMBER: combining different versions of AMBER
- AMBER: Combining Residues in LEaP for Lipid Bilayers
- AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux
- AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux. .
- AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux. .. .
- AMBER: Compile AMBER 8
- AMBER: compile amber8 on IBM-sp4
- AMBER: compile error with pgf90
- AMBER: compile error: can't locate file for: -lcrt1.o
- AMBER: compiler error for Amber9
- AMBER: compiler requirement for SGI Fuel To install AMBER9
- AMBER: Compiler with AMD 64 bit support
- AMBER: Compilers and libraries for AMBER in HPC!
- AMBER: Compiling / Installing Amber 8 on SUSE 10.1
- AMBER: Compiling Amber 9 on SGI with gcc
- AMBER: Compiling AMBER 9 on windows XP using cygwin
- AMBER: Compiling Amber8 with Sun HPC ClusterTools 5 Software
- AMBER: compiling amber9
- AMBER: compiling errors
- AMBER: Compiling Leap problem
- AMBER: compiling parallel amber 9 in linux
- AMBER: Compiling parallel Amber 9 on Red-Hat Enterprise 64 problem
- AMBER: Compiling the parallel version of amber 8 in a beowulf linux cluster
- AMBER: concatenating .mdcrd files
- AMBER: conflicting types for XawScrolledTableSetLocation
- AMBER: Confusion about PBC
- AMBER: Confusion re AMBER SMD output
- AMBER: Constant P for non-orthorhombic cells
- AMBER: constant pH simulation
- AMBER: Constant pH simulation : LYS residue
- AMBER: Constant pressure - restart - Amber8
- AMBER: constant pressure equillibration
- AMBER: convert chemical structure to pdb file
- AMBER: converting .lib files
- AMBER: converting from parm to parm7
- AMBER: converting from parm to parm7 & L-J coeff A and B
- AMBER: Coodinates not being unique
- AMBER: coordinate files
- AMBER: coordinate out of bounds
- AMBER: Correction on Zinc parameters
- AMBER: Correlation matrix used in quasih (Amber 7)
- AMBER: Cosine content calculation
- AMBER: could amber calculte the binding free energy ofonly two small ligands (no big molecules) ?
- AMBER: Could mm_pbsa decompose energy only for the receptor ?
- AMBER: Could not find atom type.
- AMBER: Could you help me about mmpbsa! thank you!
- AMBER: counterions and particle-mesh-ewald
- AMBER: CPU utilization with Parallel Sander
- AMBER: creating a RST file from specific set of binpos/crd file
- AMBER: Creating an Intercalation site
- AMBER: creating RNA, nucgen / leap
- AMBER: Curve fitting during dihedral parameter calculation
- AMBER: Curves and Average Structures
- AMBER: cutting the box after "solvatebox"
- AMBER: cyclic AMP off and frcmod files?
- AMBER: Decomposed GB energy in idecomp=3 option
- AMBER: Denaturing MD
- AMBER: density
- AMBER: Density calculation
- AMBER: desc related issue
- AMBER: description of prep file
- AMBER: Details about Gaussian basis set for Cobalt complex
- AMBER: deviations from idealized geometry
- AMBER: Did Antechamber support tertiary amines? How can I get the prepin file for it?
- AMBER: Did these differences come from so-called "different machines" ?
- AMBER: DIELC?
- AMBER: Difference in results for TI calculation
- AMBER: Different result for serial and parallel sander with IREST=1 (AMBER 8) !
- AMBER: Different results between serial and parallel runs in AMBER 8
- AMBER: Different results for TI calculation
- AMBER: different TI calculations starting from the same state
- AMBER: difficulties with antechamber: tests dont even run
- AMBER: Difficulty loading a pdb file
- AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio)
- AMBER: Dihedral analysis
- AMBER: dihedral angle equation
- AMBER: dihedral angle problem
- AMBER: dihedral calculation problem
- AMBER: dihedral parameters
- AMBER: Dimer Image Wrapping
- AMBER: DIST_RST
- AMBER: Distance between 2 atoms
- AMBER: Distance between two atoms
- AMBER: Distance between two regions
- AMBER: distance dependent dielectric constant
- AMBER: distance restraints
- AMBER: distance restraints for umbrella sampling
- AMBER: Distortion in parallelploied
- AMBER: divalent ions
- AMBER: DNA helix end stable?
- AMBER: DNA structure
- AMBER: DNA tutorial xleap help
- AMBER: DNA tutorial, in vacuo minimization
- AMBER: does anyone have library file for methylated histidine, 2003 ff?
- AMBER: does the Amber8 or Amber9 contains Br,I and Sulfur parameter for MM-PBSA or MM-GBSA.
- AMBER: DOTA-Lanthanide complexes in Amber
- AMBER: double stranded polyribocytidylic acid
- AMBER: DPPC Bilayer size
- AMBER: DRMS setting for Nmode calculation
- AMBER: Dual Xeon mpich compilation error
- AMBER: dual xeon mpich compilation problem: sorted
- AMBER: dummy atoms in MMPBSA
- AMBER: dynamic memory allocation problem in nmode
- AMBER: Dynamics and Restraint problem
- AMBER: EAMBER
- AMBER: EEL and 1-4 EEL; VDWAALS and 1-4 VDWAALS
- AMBER: EGB term decomposition
- AMBER: Electrostatic Energy Constant
- AMBER: energy conservation in NVE ensemble (ntt=0, ntb=1)
- AMBER: energy data for limited part of system
- AMBER: Energy differecnes as using igb=1 and igb=0
- AMBER: energy minimizations in amber8 vs. amber9
- AMBER: energy terms
- AMBER: entropic energy
- AMBER: Entropy calculations with Nmode and ptraj
- AMBER: erroneous placement of TER card
- AMBER: error about the number of snapshots
- AMBER: Error compiling amber on parallel (MPICH)
- AMBER: error estimate for free energy perturbation calculation
- AMBER: error GRID command in ptraj
- AMBER: error in AMBER 9.0
- AMBER: Error in compiling Amber 8 parallel
- AMBER: Error in compliling AMBER 9 on Fedora 5 linux machine
- AMBER: Error in compliling LEAP on Fedora 5
- AMBER: Error in loading molecule in tleap
- AMBER: Error in reading RDC data
- AMBER: Error in RST files in long simulations!
- AMBER: Error in running MD in sander
- AMBER: Error in Running Sander
- AMBER: Error in sysdepend.c?
- AMBER: Error in the MD run
- AMBER: error in tleap test
- AMBER: Error message in methane solvent system
- AMBER: error on running parallel sander on remote node- amber9
- AMBER: error propagation in MM-PBSA binding free energy calculation
- AMBER: Error when compiling amber9 ptraj
- AMBER: Error when installing
- AMBER: error while running sander
- AMBER: Error while running test.serial in Amber9
- AMBER: Error: cannot run "$AMBERHOME/exe/divcon" of bcc() in charge.c
- AMBER: ERROR: The PDB file is not in the working directory
- AMBER: errors in mm_pbsa.in in AMBER 8 mannul ?
- AMBER: ESP calculations.
- AMBER: Ethanol
- AMBER: Etot has downward drift in 'NVE' ensemble
- AMBER: Ewald and ibelly
- AMBER: Execution time discrepancies
- AMBER: experiences with compiling amber9 for FreeBSD
- AMBER: experiments with amber9 and fortran nag f95 on mac os x 10.4.3
- AMBER: EXTRA_PTS: frtype 2 Should not be here
- AMBER: fail to execute addles
- AMBER: failed to save prm and xyz using ff96
- AMBER: failure in testing amber8 parallel parts on IBM-SP4 machines
- AMBER: Failure of iwrap in PMEMD
- AMBER: faulty ambpdb compilation?
- AMBER: ff for drug-dna complex and drug atom types assignment
- AMBER: ff02 + POL3 problem !
- AMBER: ff02 force fields
- AMBER: ff03 and ff99SB force fields
- AMBER: ff03 GLY HAs atom type
- AMBER: ff99SB vs ff02 (ff02pol.rl)
- AMBER: FIX conformation of a ligand
- AMBER: fixing residues
- AMBER: Flag for removal of translational and rotational center-of-mass (COM) motion
- AMBER: floating point assist faults on IA64 PMEMD 9
- AMBER: For different ligand conformation
- AMBER: Force field for DNA
- AMBER: force field parameters
- AMBER: Force Field Question
- AMBER: force fields for proflavine molecule
- AMBER: force fiels for a-rna
- AMBER: Force units in forcedump.dat
- AMBER: Format of mdcrd files
- AMBER: format of qusaiharmonic eigenvector file in AMBER7
- AMBER: Format of the prmtop file (NUMBER_EXCLUDED_ATOMS) & (EXCLUDED_ATOMS_LIST)
- AMBER: forrtl: severe (64): input conversion error, unit 9, file
- AMBER: Free energy calculated from mm_pbsa
- AMBER: Free energy perturbation
- AMBER: Free energy perturbation in SANDER
- AMBER: Free-energy using MM-PBSA
- AMBER: freeze interval vibrations
- AMBER: from ADP-small protein complex to GTP-protein complex
- AMBER: from traj to crd
- AMBER: from Wei Zhang: flight information
- AMBER: Frozen at Minimization
- AMBER: Fujitsu frt compiler
- AMBER: Fully QM periodic runs
- AMBER: Fwd: ADL: peptide simulation before docking
- AMBER: Fwd: difficulties with antechamber: tests dont even run
- AMBER: Fwd: RESP for deprotonated tyrosine and lysine
- AMBER: G5 OSX serial compile error
- AMBER: G95, SGI and Amber8
- AMBER: GAFF + AM1BCC & small-molecule aggregation
- AMBER: GAFF parameters: DPPC Bilayer
- AMBER: Gaussian, antechamber, RESP
- AMBER: GB and protein backbone parameters
- AMBER: Gb Na+ ions DNA
- AMBER: GB simulation problem
- AMBER: GB tutorials and disulphide bonds
- AMBER: GBSA EGB = NaN
- AMBER: GBSA implicit chloroform
- AMBER: GBSA of nonstandard cations
- AMBER: General Coding Problem
- AMBER: General Question about Abmer
- AMBER: general question about hydrogen bond energy vs electrostatic energy
- AMBER: generalized born model for organic solvent
- AMBER: generate "template" frcmod from standard residues?
- AMBER: generating parameters for the NADH analogue H4NAD
- AMBER: generating resp input files with antechamber
- AMBER: gfortran and amber9 success on FreeBSD
- AMBER: gfortran/gcc versus ifort/icc
- AMBER: Gibbs PMF Calculation
- AMBER: GLUTATHIONE
- AMBER: GLYCAM and ff98 atom-types
- AMBER: GLYCAM and ff98 atom-types]
- AMBER: GPCR-membrane issue
- AMBER: Grid command of ptraj
- AMBER: grid output
- AMBER: Gromos to Amber
- AMBER: h bond analysis
- AMBER: h-bond
- AMBER: H-bond analysis (Ptraj)
- AMBER: H-bond analysis (Ptraj) input file
- AMBER: H-Bond Terms in amber force field
- AMBER: H-bonds of peptide with water
- AMBER: halogen bondi radii in mm_pbsa_calceneent.pm
- AMBER: Harmonic restraint along z-axis
- AMBER: have problems with restrained minimization
- AMBER: Having trouble getting Iron parameters for QM/MM
- AMBER: Having trouble with Nucgen for generating pdb more than 16 bps
- AMBER: HBON in frcmod file
- AMBER: hbond analysis
- AMBER: hbond analysis2
- AMBER: heating process
- AMBER: heating system
- AMBER: helices in GB simulations
- AMBER: helix content during my simulation
- AMBER: help creating RNA
- AMBER: help with antechamber - creating ligand
- AMBER: help with custom RNA molecule
- AMBER: help with leap
- AMBER: Help with polarization force field
- AMBER: heme improper torsions
- AMBER: Heme parameters
- AMBER: hessian calculation
- AMBER: Hessian matrix
- AMBER: Hexahydrated Counterions
- AMBER: High Values in MMPBSA
- AMBER: holding a pair of residues fixed during minimization
- AMBER: how can i treat with long "mask" in ptraj analysis.
- AMBER: How could I simulate lipid membrane with AMBER9.0?
- AMBER: How did the coordinates change in xleap?
- AMBER: How do we simulate deletion mutations
- AMBER: How does amber calculate HB?
- AMBER: How I wasted a rainy Friday in San Diego
- AMBER: How the ensemble average calculated in Gibbs, AMBER7?
- AMBER: how to add hydrogen molecules in the protein
- AMBER: How to analyze the trajectory generated by LES simulation
- AMBER: How to apply a force to some atom in a residues?
- AMBER: How to build 1,4-dimethyl benzene with amber9
- AMBER: How to build N-terminal of alanine : NH2
- AMBER: How to build NH2 of amino acid in amber
- AMBER: How to built the deprotonated form of lysine and tyrosine
- AMBER: How to calculate binding free energy using MM-PBSA
- AMBER: How to calculate RDF based on the center of mass of specific solute atoms?
- AMBER: how to calculate rmsd for non hydrogen at oms?
- AMBER: How to calculate the mmpbsa for explicit MD ?
- AMBER: how to calculate the RMSD and B-factor for all atoms of residue
- AMBER: how to choose the parameter for the production/sampling run after the equilibration run
- AMBER: how to combine NEB method with QM/MM approach
- AMBER: how to create 2'-5' RNA
- AMBER: How to create a modified NA in leap
- AMBER: How to develop charge for my deprotonated glycine
- AMBER: how to do a molecular dynamic study on a trimer
- AMBER: How to evaluate the binding energy of a ligand?
- AMBER: How to explain the meaning of the mmpbsa/DC result?
- AMBER: how to feed dihedral angles of our choice to the linear sequence in amber8
- AMBER: How to find equillibration time for my system in a generalised born solvation model
- AMBER: how to get complete prepin file
- AMBER: How to get the ligand. ac file
- AMBER: How to get the VDW contacts' messages from the mdcrd files
- AMBER: How to give the specific pressure parameter for NTP=2
- AMBER: how to include EXTRA POINTS in AMBER8
- AMBER: How to keep an hydrogen bond during an implicit MD calculation?
- AMBER: how to limit the simulation space
- AMBER: How to make a movie with .crd files in VMD?
- AMBER: How to merge two molecules to one
- AMBER: how to mutate in amber 8 for thermodynamic integration without using xleap
- AMBER: how to mutate in amber 8 for thermodynamic integration without using xleap. .
- AMBER: How to patch the configure script (macosx)
- AMBER: how to perform parallel MD on a linux cluster with Platform LSF product
- AMBER: how to reassign charges
- AMBER: How to recompile sander for single-processor use in AMBER 8?
- AMBER: how to remove the rotation of system in periodic condition?
- AMBER: how to restrain some residues in a NPT MD?
- AMBER: how to restrain the intramolecular hydrogen bond
- AMBER: How to resume remaining simulation
- AMBER: how to run a mm_pbsa on a minimized structure?
- AMBER: How to run MD simulation of a silicon containing complex with AMBER9?
- AMBER: How to run mm_pbsa_statistics.pl?
- AMBER: How to run QM/MM simulation of DNA duplex bound with platinum moietes
- AMBER: how to select the problematic residues(atoms) in VMD
- AMBER: How to set Bondi Radii using xleap
- AMBER: How to set Bondi Radii using xleap. .
- AMBER: How to simplify this big system rationally to perform MD studies
- AMBER: how to simulate water flow inside a channel?
- AMBER: How to specify a box with few walls rigid and others with periodic boundary conditions and then apply a pressure gradient across it?
- AMBER: How to specify user defined force fields or its parameters in amber??
- AMBER: How to start a Simulation of a peptide in bilayer
- AMBER: How to strip waters in trajectorie ?
- AMBER: How to submit a job in cluster
- AMBER: how to take care of toluene system neutrality
- AMBER: how to use AddPdbAtomMap
- AMBER: How to use PTRAJ to analyze the CA RMS diveations as a function of residue number?
- AMBER: How to use the prmtop and inpcrd files of ligand in a complex system?
- AMBER: How to use the prmtop and inpcrd files of ligand in acomplex system?
- AMBER: Hybridization in leap
- AMBER: hydronium ion parameters
- AMBER: I got the error meassage in testcase of QMMM
- AMBER: I'm very sorry, please disregard previous e-mail--problem seems to be fixed
- AMBER: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031
- AMBER: ibelly & fix atom
- AMBER: ibelly not work
- AMBER: identical high energies
- AMBER: IGB=10
- AMBER: igb=2 and "bad atom type" conflict
- AMBER: Ignoring every other frame in a .crd trajectory in Ptraj
- AMBER: imaging issue
- AMBER: implicit solovent model by adjusting the parameter EXTDIEL ?
- AMBER: Implicit solvent question
- AMBER: Implicit Water - Force field parameters
- AMBER: impose command in leap problem
- AMBER: improper torsion angle problem
- AMBER: Impropers definition
- AMBER: inconsistence in MM_PBSA between mm_pbsa .pl and mm_pbsa_statistics.pl
- AMBER: increase force constants
- AMBER: increase in computational time with LES
- AMBER: individual torsion/bond energies from a minimization
- AMBER: Info regarding reduced cysteines
- AMBER: input conversion error mm_pbsa
- AMBER: Input conversion error.
- AMBER: install error
- AMBER: Installation amber 9 on IBM SP4
- AMBER: Installation amber 9 on IBM SP4; bugfix 12
- AMBER: installation error for pmemd in Amber 9/Opteron
- AMBER: Installation help - SGI Altix 350
- AMBER: Installation of AMBER8 on a PC with a Pentium EE type
- AMBER: Installation of AMBER8 on a PC with a Pentium EE type CPU
- AMBER: Installation of Amber8 on Fedora Core 5
- AMBER: Installation of Amber8 on Fedora Core 5. .
- AMBER: installation problem
- AMBER: Installing / Compiling Question
- AMBER: Installing Amber 9 on Mac Pro
- AMBER: Installing AMBER9 on cygwin (WinXP)
- AMBER: Installing Delphi to perform mm_pbsa analysis?
- AMBER: instructions for making a library file for an unusual residue?
- AMBER: Intel compiler version 9.0.033
- AMBER: Intel fortran compiler 7?
- AMBER: Interaction Energy Calculation
- AMBER: Interbox interactions
- AMBER: internal coordinates
- AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions?
- AMBER: ions+proteins
- AMBER: Is GB/SANDER slower than TIP3P/PMEMD
- AMBER: is seems that The SAS in MMPBSA is SES , not SAS. ????
- AMBER: Is there a way to simulate a box of pure water with amber
- AMBER: is there any relationship between RMSD and B-factor?
- AMBER: Is there anyway to recover the LISTOUT obtained after running a md with nmr restrictions
- AMBER: iso command and a cubic box
- AMBER: Issue with installation of Amber v9.0 parallel compilation
- AMBER: Istallation AMBER8
- AMBER: ISTRNG or SALT in MM_PBSA
- AMBER: job crashes
- AMBER: k-space cutoff with standard Ewald
- AMBER: kclust
- AMBER: kill job command?
- AMBER: klambda
- AMBER: klambda for TI method.
- AMBER: Langevin mode error??
- AMBER: Langevin temperature control vs berendson heat bath
- AMBER: Leap
- AMBER: LEAP - "could not find type: NH"
- AMBER: leap - compilation error
- AMBER: leap - how to recognize my structure
- AMBER: Leap adds hydrogens but cannot resolve their type.
- AMBER: leap can't assign CALA
- AMBER: Leap compilation issues
- AMBER: LEAP error
- AMBER: LEAP error (Test Case)
- AMBER: LEaP error : unbalanced charge
- AMBER: LEaP not recognising Phosphate group in TYR
- AMBER: LEaP problem
- AMBER: leap usage
- AMBER: LEaP Warning ... when do NH2-neutral fragment
- AMBER: Leap: neutralising the charge
- AMBER: leap: syntax error when use source command
- AMBER: LENNARD_JONES_ACOEF & BCOEF prmtop changes
- AMBER: LES copies
- AMBER: LES error
- AMBER: lib file
- AMBER: lib-4324 : UNRECOVERABLE library error
- AMBER: library for 8oxoguanine
- AMBER: lifetime and maxocc
- AMBER: lifetimes
- AMBER: Ligand charge
- AMBER: ligand file
- AMBER: lipid bi-layer system
- AMBER: load charges to antechamber calculations
- AMBER: loading torsion parameters
- AMBER: LogP
- AMBER: Long line of input
- AMBER: m4 error with Amber8 on SUN
- AMBER: Machine File for Intel Core 2 Duo E6400
- AMBER: Macromodel Amber* vs. Amber7
- AMBER: Making sure that Amber jobs use Infiniband?
- AMBER: manual docking
- AMBER: manual/prmtop/missing bonds section
- AMBER: mask issues
- AMBER: Mass weights
- AMBER: Mass wieghted Covariance Matrix
- AMBER: matrix correl
- AMBER: Maximum system size in simulated annealing
- AMBER: MAXM in nmode
- AMBER: md and implicit solvation
- AMBER: MD and MMPBSA
- AMBER: md error : sander
- AMBER: MD job stopped without any error information?
- AMBER: MD of oligomer sequences
- AMBER: MD on protein-ligand interaction
- AMBER: MD stopped
- AMBER: MD with positional and NMR restraints
- AMBER: MD with restraint (nmropt=1)
- AMBER: mdcrd file
- AMBER: Middlebury College Cluster and Amber 8
- AMBER: minimalization prior to nmode analysis, is it necessary?
- AMBER: minimization of Hydrogens with xLeaP
- AMBER: Minimization problem: coordinates out of virtual box
- AMBER: minimization with my own charges
- AMBER: minization: outputing intermediate snapshots
- AMBER: Minizsation strange error message! Please help.
- AMBER: missing benchmark files
- AMBER: Missing LES reference in Amber 9 manual
- AMBER: Missing values for MM VDW
- AMBER: missing values in md.out
- AMBER: Mixed solvent?
- AMBER: mixing GAFF and CHARMM
- AMBER: MM-GBSA decomposition
- AMBER: MM-PBSA
- AMBER: MM-PBSA and first solvation shell
- AMBER: MM-PBSA and gaff atom types
- AMBER: MM-PBSA memory usage
- AMBER: mm-pbsa output
- AMBER: MM-PBSA problem
- AMBER: MM-PBSA questions
- AMBER: mm-pbsa: distant-dependent dielectric constant
- AMBER: MM-PBSA: Problem when Generating Snapshots
- AMBER: MM/PBSA
- AMBER: MM_PBSA
- AMBER: MM_PBSA : Question about Stability?
- AMBER: mm_pbsa calculation allocation error
- AMBER: mm_pbsa calculation for calcium
- AMBER: mm_pbsa does not terminate
- AMBER: MM_PBSA error
- AMBER: mm_pbsa output
- AMBER: mm_pbsa PBCAL
- AMBER: MM_PBSA problem (No values for MM_GAS )
- AMBER: mm_pbsa problem in IBM-aix
- AMBER: mm_pbsa reference
- AMBER: mm_pbsa segmentation faults
- AMBER: mm_pbsa snapshots for "three-trajectory"
- AMBER: mm_pbsa.pl fails to start in linux cluster
- AMBER: mm_pbsa: "Missing values for MM ..."
- AMBER: mm_pbsa: binding energy calculation
- AMBER: MM_PBSA: “Found unknown atflag DELPHI”
- AMBER: mm_pbsa_statistical.pl
- AMBER: MMPBSA
- AMBER: MMPBSA & PBCAL
- AMBER: MMPBSA entropy question
- AMBER: MMPBSA error
- AMBER: mmpbsa in parallell
- AMBER: MMPBSA problem
- AMBER: MMPBSA vDW error
- AMBER: mmpbsa: fail to run heat in tutorial A3
- AMBER: MMPBSA: magnitude of PB calculation
- AMBER: MMPBSA: positive energies during nmode
- AMBER: MMTSB: phi-pdi-based clustering
- AMBER: modeling a non-standard molecule.
- AMBER: modeling of ligand concentrations
- AMBER: modeling zinc binding site
- AMBER: Modelling dsDNA less than 10bp
- AMBER: Modify charges to increase/decrease hydrogen bond interaction
- AMBER: Modifying a Force Field
- AMBER: molsurf or LCPO method in MM_GB/SA?
- AMBER: molsurf.c error
- AMBER: monosaccharide residues
- AMBER: More Amber 9 Benchmarks available
- AMBER: MPI parallel problem in AMBER 8.0
- AMBER: mpich Amber7 problem
- AMBER: MPICH and Sander
- AMBER: MPICH on OpenMosix
- AMBER: MPICH-1.2.7 compilation problem !
- AMBER: multiple "restraint_wt" in sander
- AMBER: Multiple Timestep MD
- AMBER: Mutual exclusion of atoms
- AMBER: Myrinet or Gigabit ethernet?
- AMBER: N-H and C-H Residual Dipolar Coupling
- AMBER: N1-protonated adenosine, N-terminal myristyl group
- AMBER: Na+ with GB/SA?
- AMBER: NAD ??
- AMBER: NAD parameters
- AMBER: NADP(H) parameters
- AMBER: Namelists in input files
- AMBER: NAMOT
- AMBER: Namot on AMD 64 possible
- AMBER: Nature of QM scanning protocol for parameter development
- AMBER: Need to know meaning of numbers in parm99.dat file to be able to write frcmod file for dummy atoms
- AMBER: negative T_solv values
- AMBER: negative values of PBSOL and PBCAL in mm_pbsa result
- AMBER: neutral N-terminal amino-acid parameters for ff03
- AMBER: New (small) Topology without solvent from previous one (big) with solvent
- AMBER: new article on Amber force fields
- AMBER: New united atom force field and GB solvation model in amber9 (leaprc.ff03ua)
- AMBER: NEWPDB.PDB from antechamber
- AMBER: NGL error when creating snapshots for MM/PB(GB)SA
- AMBER: nmode calculations error
- AMBER: nmode different units
- AMBER: nmode memory allocation error
- AMBER: Nmode memory allocation error ?
- AMBER: Nmode memory allocation problem
- AMBER: nmode memory problem
- AMBER: nmode output with ptraj
- AMBER: Nmode vs QM Freq Calculation
- AMBER: nmode: number of atoms limitation
- AMBER: NMR restraint
- AMBER: NMR restraints and LES
- AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5?
- AMBER: non bond list overflow
- AMBER: Non bond list overflow in amber8.0 program.
- AMBER: Non-periodic simulations: How is the system kept together?
- AMBER: NONB values adjusted?
- AMBER: nonplanarity of NH2 groups
- AMBER: Not getting proper structure after minimization
- AMBER: NTR for implicit solvent? How to defin restrain for two disconnected sequences?
- AMBER: NTR for implicit solvent? How to defin restrain for two disconnectedsequences?
- AMBER: NTT for production run
- AMBER: ntt=1 in simulated annealing
- AMBER: nucgen error
- AMBER: Nucgen Problem
- AMBER: Obtaining an average structure from a trajectory
- AMBER: Obtaining LCPO parameters for F and Fe
- AMBER: offset?
- AMBER: on rst file
- AMBER: on the rst file of the current ruuning
- AMBER: On the temperature increasement in the restriction MD in the tutorial 2 section 5
- AMBER: one question about mm_pbsa
- AMBER: one question on MD
- AMBER: Oon Modeling the metalloprotein with GB model.
- AMBER: openmpi
- AMBER: opls_aa in amber
- AMBER: Opteron vs. Xeon performance
- AMBER: optimatized structure is so much different from the original pdb structure
- AMBER: organic molecule - from newbie :)
- AMBER: Organic molecules
- AMBER: OSX 10.4 G4 xlf90 compilation errors
- AMBER: OT: software to support AMBER?
- AMBER: output file not generated
- AMBER: output of first stage RESP calculation
- AMBER: paralelization and sander problems
- AMBER: parallel compile problems on amber8
- AMBER: Parallel compile: ld: cannot find -lfmpi
- AMBER: parallel computation time vs serial computation time
- AMBER: Parallel error in Amber 8
- AMBER: parallel installation of amber8 on HP cluster
- AMBER: parallel pmemd with intel 9 fc
- AMBER: parallel problem of amber8
- AMBER: Parallel version of Amber: error message
- AMBER: Parallelization method
- AMBER: parameter definitions
- AMBER: parameter for Cd2+?
- AMBER: parameter loading problem
- AMBER: PARAMETERISATION PROBLEM
- AMBER: Parameterization of ethidium - phenyl ring
- AMBER: parameters !!??
- AMBER: parameters for beta peptides
- AMBER: parameters for C=S
- AMBER: parameters for fluoromolecules with more than one single carbon?
- AMBER: Parameters for Nickel
- AMBER: parameters for Nickel and iron
- AMBER: parameters for silicon atom
- AMBER: parm*.dat
- AMBER: parmchk error
- AMBER: Parmchk problems (parm99.dat)
- AMBER: Parmtop file: ANGLE_EQUIL_VALUE actually in radians?
- AMBER: partial charge glycam
- AMBER: partial charges
- AMBER: passwordless ssh stopped working
- AMBER: PB bomb in pb_atmlist(): MAXNEI too short
- AMBER: PBS script for lemieux
- AMBER: PBSA calculation fail ....
- AMBER: pbsa segmentation faults
- AMBER: PCA
- AMBER: PCA analysis
- AMBER: PCA and projections
- AMBER: PCA results with explicit Vs Implicit solvation
- AMBER: PCA: can't complete projection
- AMBER: pdb error
- AMBER: PDB from .rst?
- AMBER: peptide simulation before docking
- AMBER: Performing Interactive Essential Dynamics in Ptraj
- AMBER: Performing Simulated Annealing?
- AMBER: Periodic boundary condition (PBC)
- AMBER: Periodic boundary condition (PBC) > Problem now with ptraj
- AMBER: periodic boundary condition in the X and Y dimensions only
- AMBER: periodic boundary condition question...
- AMBER: Periodic simulations with net charge
- AMBER: perturbed and unperturbed charges
- AMBER: phantom sander8 in dmesg
- AMBER: Phenyl Ring atom types
- AMBER: Phosphated Tyrosine, not a type (xleap)?
- AMBER: Phosphorylated amino acid
- AMBER: Phosphorylated protein MD simulation
- AMBER: PhosphoThreonine Parms for use with ff03
- AMBER: Picking up water molecules around one molecule
- AMBER: PKDIV lone pair dihedrals
- AMBER: Please DISREGARD previous message (restraint=0.0000)
- AMBER: Please reply
- AMBER: PMED in AMBER
- AMBER: PMEMD and OpenMPI, anyone have config options?
- AMBER: PMEMD compilation error
- AMBER: pmemd error
- AMBER: pmemd installation on linux_p3_athlon ifort
- AMBER: pmemd installation problem
- AMBER: PMEMD MPI_Finalize() error
- AMBER: PMEMD scaling
- AMBER: PMEMD with NMR restraint and position restraint
- AMBER: pmemd9 issue
- AMBER: pmemd_parallel_ins_prob
- AMBER: pmf input files
- AMBER: pmf with respect to a surface
- AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next?
- AMBER: PO2 in a DNA fragement, not a type in xleap? What canI do next?
- AMBER: polarizable ff for ligand
- AMBER: polarization effects
- AMBER: POPC parameters
- AMBER: positional restraints & constant pressure
- AMBER: post nmanal
- AMBER: Post-MD minimization
- AMBER: post-processing replica exchange trajectory
- AMBER: potential energy
- AMBER: Potential Energy Calculation
- AMBER: potential energy in the MD result
- AMBER: Potential of Mean Force calculation or Steered molecular dynamics
- AMBER: Power Mac G5
- AMBER: pqr file
- AMBER: pqr from constant pH MD
- AMBER: prep files for L-sugar residues
- AMBER: preparing ligand/rna structure for MD
- AMBER: prepi definitions
- AMBER: prepin file nan
- AMBER: prepin format
- AMBER: Pressure in MD
- AMBER: Pressure problem with restraint
- AMBER: printing Amber VdW radii as separate column in pdb files
- AMBER: probable bug in antechamber
- AMBER: Probelm with running Amber 9 parallelly
- AMBER: problem about Distance Restraints.
- AMBER: Problem about dummy atoms when running antechamber
- AMBER: Problem about installing amber9 on Mac OS X
- AMBER: problem at the start of heating up (using extra-point)
- AMBER: problem imposing arbitrary peptide bonds through leap
- AMBER: Problem in Antechamber
- AMBER: problem in calculating EGB using sander for ligand containing F atom
- AMBER: problem in center command
- AMBER: Problem in compiling AMBER8 parallel version
- AMBER: Problem in compiling sander with MMTSB
- AMBER: Problem in running umbrella sampling
- AMBER: problem in saving parameter file for non-standard residue
- AMBER: Problem Installing Amber in SGI Irix 6.5
- AMBER: problem installing amber9 with g95 gcc on a fc5 m/c
- AMBER: problem loading forcefield leaprc.ff86
- AMBER: Problem loading peptoid residues with antechamber
- AMBER: problem of installing carnal on macosx
- AMBER: Problem of Ptraj in AMBER9
- AMBER: Problem of QM/MM calculation with amber 9 parallel version
- AMBER: problem of the REMD with nmr constraints
- AMBER: problem relating all atom structure prediction and folding simulations on AMBER8
- AMBER: Problem taking the PDB to the Amber coordinates for calculations
- AMBER: problem to center solvateshell
- AMBER: Problem using antechamber
- AMBER: Problem with "impose" in leap
- AMBER: problem with amber 9 and igb=5
- AMBER: Problem with bcc flag of antechamber
- AMBER: Problem with bcc flag of antechamber..continued
- AMBER: problem with calcpka.pl
- AMBER: Problem with donor/acceptor specification in ptraj hbonding facilities
- AMBER: Problem with file size of sander outputs
- AMBER: Problem with impose in lep
- AMBER: problem with installation, or bug?
- AMBER: Problem with LEaP
- AMBER: Problem with mask when using distance in ptraj
- AMBER: problem with NAD+ parameters
- AMBER: problem with pattern searching in mm_pbsa_calceneent.pm, Amber8, when salt>0 using delphi version 4
- AMBER: problem with prep file
- AMBER: problem with prepfile
- AMBER: Problem with ptraj
- AMBER: Problem with restarting MD simulation
- AMBER: Problem with running xleap remotely
- AMBER: Problem with sander in Linux
- AMBER: problem with saving the parameters file
- AMBER: Problem with setbox command...
- AMBER: Problem with shared libraries: libimf.so
- AMBER: Problem with specifying NOSHAKEMASK
- AMBER: problem with ssh and xleap
- AMBER: problem with the output file for free energy perturbation calculation
- AMBER: Problem working with Antechamber
- AMBER: Problem: Flag "SOLVENT_POINTERS" not found in PARM file
- AMBER: problems about compiling a parallel version of AMBER 9
- AMBER: Problems amber mask in distance?
- AMBER: Problems compiling amber9
- AMBER: problems for running sander.MPI
- AMBER: problems of running sander.MPI of amber9 on remote node
- AMBER: problems on mm_pbsa
- AMBER: problems trying to modify Amber8
- AMBER: Problems using rst distance constraints in Amber 8
- AMBER: Problems with a restrained minimization approach
- AMBER: problems with antechamber
- AMBER: problems with Calcium ions treatment in GB run
- AMBER: Problems with carnal (Amber7)
- AMBER: problems with cpinutil.pl
- AMBER: Problems with equilibrating the starting density
- AMBER: problems with ptraj
- AMBER: Problems with restart file from pmemd sim.
- AMBER: problems with saveamberprep command
- AMBER: problems with saving self-built molecules parameters
- AMBER: process_mdout
- AMBER: process_mdout.perl
- AMBER: process_mdout.perl error
- AMBER: process_mdout.perl's output is empty
- AMBER: program to calculate net charge of a ligand for Antechamber
- AMBER: Programes to calculate ligand RMSD
- AMBER: proper restart procedure?
- AMBER: proposed patch for ptraj/evec.c (Amber 9.0)
- AMBER: protein ligand complex
- AMBER: protein-ligand interaction
- AMBER: protocols for NMR protein refinement with AMBER
- AMBER: protonated phosphate
- AMBER: Pt containing complex: antechamber
- AMBER: Pt containing complex: xleap
- AMBER: ptraj
- AMBER: Ptraj & pca
- AMBER: ptraj and mdvel question
- AMBER: ptraj atomicfluct
- AMBER: ptraj atomicfluct: is it possible to calculate atomic fluctations from a reference structure
- AMBER: ptraj distance matrix
- AMBER: ptraj dumpq feature/bug
- AMBER: PTRAJ generating wrong dihedral angles
- AMBER: ptraj grid
- AMBER: ptraj grid output
- AMBER: ptraj hbond analysis troubles
- AMBER: ptraj help - amber7 failed, amber8 read prmtop file incorrectly...
- AMBER: ptraj help - ERROR in readParm: ... failed to find CHARGE
- AMBER: ptraj mask question
- AMBER: PTRAJ OUTPUT
- AMBER: ptraj PCA
- AMBER: ptraj PCA: projection mask bug??
- AMBER: Ptraj problems
- AMBER: ptraj quasiharmonic analysis question
- AMBER: ptraj radial problem: Segmentation fault
- AMBER: Ptraj reimage truncated octahedral box simulation with AMBER8
- AMBER: PTRAJ RMS: dumping RMSd vs time data
- AMBER: ptraj RMSD vs. RMSF
- AMBER: ptraj script
- AMBER: Ptraj selecting specific atoms in specific residues
- AMBER: Ptraj syntax change Amber8->Amber9 ?
- AMBER: ptraj vector
- AMBER: ptraj vector corrplane bug
- AMBER: ptraj warning while loading reference
- AMBER: ptraj----radial output files
- AMBER: ptraj: calculating distances between atoms in charges residues
- AMBER: Ptraj: correlation time
- AMBER: Ptraj: diffusion rate
- AMBER: ptraj: hbond analysis
- AMBER: Ptraj: Hbond time series
- AMBER: ptraj: nofit option for rmsd
- AMBER: Ptraj: radial distribution and correlation coefficient
- AMBER: PTRAJ: radius of gyration
- AMBER: ptraj: rms per residue
- AMBER: ptraj:hbond question
- AMBER: puzzles about solvatoct or solvatebox
- AMBER: Q: results from PB solver in example no.3
- AMBER: Qestion about input for RESP program
- AMBER: QM/MD energy conservation
- AMBER: QMMM simulation
- AMBER: Quantifying pi-pi interactions
- AMBER: Question about .off file
- AMBER: question about building molecules
- AMBER: Question about Energy calculation using MM-PBSA scripts & Imaging
- AMBER: Question about free energy with mm_pbsa
- AMBER: question about group format
- AMBER: Question about interpretation of sander.QMMM results
- AMBER: Question about LEAP and twisting a dihedral angle
- AMBER: Question about NSCM
- AMBER: Question about ptraj setup for phase angles (P) of ribose sugar puckering
- AMBER: question about QM/MM in amber9
- AMBER: question about REDII
- AMBER: Question about renaming a residue
- AMBER: Question about sander code
- AMBER: question about solvatecap commander
- AMBER: Question about Streptavidin/Biotin Tutorial.
- AMBER: question about the topology file
- AMBER: Question about using antechamber with G03
- AMBER: Question about using PMEMD and GB
- AMBER: Question bonds and angles in frcmod and lib files
- AMBER: Question bonds and angles in frcmod and lib files]
- AMBER: question capping helix ends
- AMBER: question on chargning free energy in solvent vs vacuum
- AMBER: question on chargning free energy in solvent vs vacuum. .
- AMBER: question on distance calculation
- AMBER: question on Lennard-Jones fitting in FF94 and 96
- AMBER: question on mm_pbsa_statistics.pl
- AMBER: question on molsurf
- AMBER: question on protein folding simulation
- AMBER: Question regarding lastrst and taup
- AMBER: Questions
- AMBER: questions about mm_pbsa
- AMBER: questions on mm_pbsa_statitistics.pl
- AMBER: Questions/observations about Nudged Elastic Band (NEB)
- AMBER: quistions about pbsa cacultaion
- AMBER: R.E.D II
- AMBER: Radius of gyration
- AMBER: rbornstat average and fluctuations incorrect when nrespa != nrespai
- AMBER: RDC refinement
- AMBER: RDF calculation
- AMBER: RDF output
- AMBER: RDF problem
- AMBER: RDII and epsilon of ho and hw wrong in gaff.dat ??!!!
- AMBER: rdparm
- AMBER: reading ff file into XLeap
- AMBER: reading psf file
- AMBER: recompiling bondtype.C
- AMBER: reconstructing PMF
- AMBER: RED - help with installation / config
- AMBER: Reducind trajectory
- AMBER: Reducing trajectory
- AMBER: reference of ff99
- AMBER: references
- AMBER: regarding diffusion command output
- AMBER: regarding Hydrogen bond analysis
- AMBER: regarding PBCAL in MM-PBSA
- AMBER: reinstall amber8
- AMBER: Related to RESTRAINT_WT
- AMBER: Release of RESP ESP charge DDatabase
- AMBER: REM test failures on IA-64 architecture
- AMBER: REMD: Hybrid topology file
- AMBER: remlog option changed in amber9?
- AMBER: Renumber residues in LEAP
- AMBER: repeat use of a trimer lib file
- AMBER: Replica exchage: about exchange interval
- AMBER: Replica Exchange
- AMBER: replica exchange hangs
- AMBER: Replica exchange rate in REMD
- AMBER: Replica exchange with Amber9
- AMBER: requirement of delphi for mm_pbsa
- AMBER: residence time of water molecules
- AMBER: residence time& hydration density
- AMBER: residue and atom number
- AMBER: Residue connection points on prep.in
- AMBER: resolving a bad initial model
- AMBER: resp
- AMBER: RESP charge fitting
- AMBER: RESP charge fitting for HFIP
- AMBER: RESP charge fitting problems with capping group
- AMBER: RESP charges of iron-porphyrin system
- AMBER: RESP problem
- AMBER: RESP procedure for DMPC monomer
- AMBER: Respgen segemtation fault
- AMBER: respin file
- AMBER: Restart problem on PMEMD with position restraint.
- AMBER: Restarting constant pressure sims with restraints
- AMBER: Restarting with new topology
- AMBER: Restraint internal coordinates in Amber 8.0
- AMBER: restraint=0.0000 during minimization?
- AMBER: restraintmask
- AMBER: restraints and constant pressure
- AMBER: Restraints of the strand-endings?
- AMBER: Review.
- AMBER: rgbmax--something wrong with my input file?
- AMBER: Ring of dna
- AMBER: Ringof dna
- AMBER: RMS
- AMBER: RMS & PCA
- AMBER: RMS (fwd)
- AMBER: RMS FLUCTUATIONS
- AMBER: rms in principal component analysis
- AMBER: rms processing
- AMBER: RMSD calculation between ligands
- AMBER: RMSd calculations
- AMBER: RMSd error
- AMBER: rmsd value for organic molecule
- AMBER: RMSd vs RMSf
- AMBER: RMSD: is it related to flexibility?
- AMBER: running sander on several nodes
- AMBER: saltcon variable
- AMBER: saltcon with explicit water?
- AMBER: saltconc for explicit solvent calculation.
- AMBER: San Fransisco Amber users
- AMBER: sander error about fortran
- AMBER: sander error: rst file crash
- AMBER: Sander NOE violations
- AMBER: sander ntc=2 ntf=1
- AMBER: sander problem
- AMBER: sander restart problem
- AMBER: sander testing problem
- AMBER: Sander--NMR refinement
- AMBER: sander/topology problem
- AMBER: sander: cannot execute binary file
- AMBER: save coordinates during SANDER minimisation
- AMBER: saveamberparams error in Amber9
- AMBER: SAVEPDB in Xleap could not save 4 character atom names
- AMBER: Saving RMSD values in VMD
- AMBER: Saving single coordinate set from Amber trajectory file as a restrt file.
- AMBER: script advice
- AMBER: script to extract data from minimization .out file
- AMBER: Second derivative matrix
- AMBER: seg fault during test.serial
- AMBER: Semi-empirical parameterization -- van der Waals and H-bonding?
- AMBER: separating LES copies in moil view
- AMBER: sequential execution of number of parallel jobs
- AMBER: set a trucated octahedron box in Leap
- AMBER: setBox with buffer in leap
- AMBER: Setting box dimensions in leap
- AMBER: SGI compiler problems
- AMBER: SHAKE - ntc = 3
- AMBER: SHAKE problem after minimization
- AMBER: Shake&Lone Pairs
- AMBER: SHAKE, TIP3P and 2fs Timesteps
- AMBER: Shared libraries error
- AMBER: Silicon related parameters
- AMBER: simulate a self-assemble process in vacuum
- AMBER: simulate proteins with non-standard residues
- AMBER: Simulated Annealing problem...
- AMBER: simulated annealing run--temp won't rise
- AMBER: Simulating a periodic crystal
- AMBER: simulating a small chain protein in water box
- AMBER: Simulating an "average" DNA sequence
- AMBER: Simulating proteins with calcium ion
- AMBER: Simulation a small chain of amino acids - error in MD simulation
- AMBER: Simulation of crystal - problem with excluded atom list
- AMBER: simulation of protein in non-aq or organic solvent bath
- AMBER: single or dual topology for TI?
- AMBER: small bug in ambmask (amber9)
- AMBER: Snapshots (pdbs) from a trajectory.
- AMBER: soft-core potential in amber?
- AMBER: software to visualize normal modes
- AMBER: Solvating a bilayer
- AMBER: Solvating the system with specific number of water molecules...
- AMBER: solvation and His protonation
- AMBER: Solvation Energies
- AMBER: some new tutorials
- AMBER: some puzzles in equilibration MD
- AMBER: some questions and problems about antechamber and divcon
- AMBER: Some warning !!! during SANDER ?
- AMBER: source code
- AMBER: specifying RSOLV when calculating 2003 force field charges
- AMBER: splitting LES with ptraj in amber9
- AMBER: Steered molecular dynamics with Amber 8.0
- AMBER: Strange minimization output problem
- AMBER: strange mm_pbsa output
- AMBER: Strange problems with PMEMD on Intel Xeons with Infiniband
- AMBER: strange result of mm/pbsa
- AMBER: strange temperature behavior when changing to constant pressure
- AMBER: strange values of the energy of "1-4 EEL" , "EAMBER" and the RMS
- AMBER: strange values of the energy of "1-4 EEL" , "EAMBER" andthe RMS
- AMBER: stripping trajectories: ptraj versus Carnal
- AMBER: structure from MD
- AMBER: Suitable water box
- AMBER: Sulfonamides and GAFF
- AMBER: SURFTEN in GB (mm_pbsa calculations)
- AMBER: SURFTEN/SURFOFF values in amber9
- AMBER: switching function for electrostatic interactions
- AMBER: System in polarizable waters
- AMBER: temp control
- AMBER: Temperature fluctuation BIG with ntt=3
- AMBER: Temperature fluctuation with Langevin Temperature control
- AMBER: Temperature not rising enough during simulated annealing
- AMBER: temperature regulation
- AMBER: terms in mm-pbsa
- AMBER: Test Failure during amber9 serial compilation
- AMBER: Test Message Please Ignore
- AMBER: Test Message Please Ignore.
- AMBER: tetrolic acid
- AMBER: TFE parameters for Amber
- AMBER: the best force field for DNA
- AMBER: the energy and temperature both increasing during the simulation with NTT=0
- AMBER: the parallel efficiency of my sander and pmemd descended rapidly with increasing CPUs
- AMBER: The PB GB energy from mm_pbsa will be positive on high charged system
- AMBER: The plc.frcmod file in the old version tutorial
- AMBER: the problem of mdcrd
- AMBER: the RMSD of MD
- AMBER: the sequence command in leap
- AMBER: the time length of the restricted MD
- AMBER: the total energy is not converge as the cutoff increase
- AMBER: The VDW correctioin
- AMBER: Thermodynamic integration using the amber 9
- AMBER: TI cal
- AMBER: Ti calculations in dmso solvent
- AMBER: TI tutorial
- AMBER: TI vlimit exceeded
- AMBER: TI, mutation
- AMBER: TI-FEP : strange result for different clambda values
- AMBER: TI-FEP for ILE--->VAL.
- AMBER: timing estimates
- AMBER: tleap BUG to write a pdb file if atom name contains 4 chars.
- AMBER: To create methanol solvent box
- AMBER: to do tutorial 4 using tleap
- AMBER: too big EEL values in the minimisation output
- AMBER: top2mol2.c scanf format string bug
- AMBER: Torsional restraints for groups of atoms
- AMBER: trajin and rms
- AMBER: trajout
- AMBER: trajout script
- AMBER: transition metals and the parmcal of the antechamber module
- AMBER: transition state
- AMBER: tree name generated by tleap is different from the input PREP parameter file
- AMBER: Trimming ptraj output
- AMBER: trouble adding mdcrd files together
- AMBER: trouble stripping waters with ptraj
- AMBER: Trouble with combining a non-standard residue with a protein of standard residue
- AMBER: Trouble with Leap
- AMBER: Trouble with ptraj closestwater in Amber8
- AMBER: Truncated octahedral box as triclinic lattice vectors
- AMBER: Tutorial 2 - Section 4: Summary.density and summary.temp
- AMBER: Tutorial 2: Minimise and equlibrium error NaN
- AMBER: Tutorial 2: Production MD.
- AMBER: Tutorial 4-section 4 (plc.frcmod)
- AMBER: Tutorial 4-section 4 - VDW parameters
- AMBER: Tutorial 4-section 4 DIHE in frcmod file.
- AMBER: Tutorial 8, section 6: best fit before clustering
- AMBER: Tutorial one : libsvml.so error
- AMBER: Tutorial one : xaLeap command not found.
- AMBER: Two different HIS ligands
- AMBER: two references
- AMBER: two references- I got them, thank you!
- AMBER: Umbrella sampling
- AMBER: Unable to find mopac charges in divcon.out
- AMBER: Unable to find solution for an error - "cannot successfully assign bond type"
- AMBER: Unit 5 Error on OPEN: md.in
- AMBER: Unit of force
- AMBER: united atoms
- AMBER: Units for Leonard-Jones potential parameters
- AMBER: Unstable RMS trajectory
- AMBER: Updated Tutorials Page
- AMBER: use ptraj and two differenct prmtop file to analyze LES trajectory
- AMBER: use_pme=0 problem
- AMBER: Using a trajectory and some PDB files as input for PCA
- AMBER: using MM_PBSA just for binding site, feasible ???
- AMBER: Using modified NA bases
- AMBER: Using XML for Amber files
- AMBER: Values of Spring Constants
- AMBER: VdW radii in the topology file
- AMBER: Virus?
- AMBER: vlimit exceeded
- AMBER: vlimit exceeded for step 0, vmax = infinity
- AMBER: VMD PDB into LEAP Readable PDB
- AMBER: Volume of ucell too big
- AMBER: Water density output
- AMBER: water diffusion
- AMBER: water molecules with in 3 angstroms to the solute
- AMBER: water prmtop/inpcrd problem
- AMBER: waters closest to specific residues
- AMBER: watershell and image commands
- AMBER: watershell command
- AMBER: WHAT IF CHeck after MD
- AMBER: what is the integration scheme for langevin dynamic used in amber8
- AMBER: what is the RMS value in resp charge fitting ?
- AMBER: what is unit of the out put of mmpbsa caculation
- AMBER: what to do with the counter ions when minimizing average structure of DNA?
- AMBER: What Viewer is best
- AMBER: What's going wrong when I use antechamber dealing with lipid molecular?
- AMBER: What's the meaning of NTYPES?
- AMBER: WHATIF Check after MD
- AMBER: where can I find the force field paramete r for Silica
- AMBER: Where can I find the SMD parameter file (or simple turtorial) in AMBER9
- AMBER: Where is the repulsion energy ( part of nonpolar solvation energy) in MM_PBSA ?
- AMBER: Where to modify the atom type in sander?
- AMBER: where to set bondi radii for halogens
- AMBER: Which one is the best force field for DNA?
- AMBER: which patch for ioutfm = 1 in Amber8?
- AMBER: Which POPC Bilayer to start?
- AMBER: Which PTRAJ distribution to use?
- AMBER: which time should I use to calculate the number of "ps/Day"
- AMBER: Why "ho" and "hw" VDW's radius are set to 0 in "gaff.dat" ?
- AMBER: why has "ELE " a large fluctuation in MMP BSA?
- AMBER: why has "ELE " a large fluctuation in MMPBSA?
- AMBER: why the drms from sander minimization is not consistent with that from nmode ntrun=1?
- AMBER: Why the energy from sander minimization (epsilon=4r) is not same with that from nmode, when restraint is applied?
- AMBER: why the perturbation from PHE to ALA is not stable with gibbs, amber 7
- AMBER: Why the result from sander minimization (epsilon=4r) is not same with that from nmode, when restraint is applied?
- AMBER: working with large strained system
- AMBER: Workshops
- AMBER: xleap
- AMBER: Xleap 64 bit installation problem
- AMBER: Xleap compilation problem
- AMBER: Xleap crash
- AMBER: xleap not recognizing residue
- AMBER: xleap not recognizing residue--I fixed it, but I'm not sure why
- AMBER: xleap on iMac G5
- AMBER: xleap problem
- AMBER: xleap problem and answer
- AMBER: xleap problems
- AMBER: Xleap woes
- AMBER: xleap, generating prep file
- AMBER: xmgr error
- AMBER: Xmgr in Windows
- AMBER: zero entry in LENNARD_JONES_ACOEF of prmtop files
- AMBER: Zinc coordinating CYS
- AMBER: Zinc parameters
- AMBER: Zinc-coordinating histidine protonation state
- AMBER: Zn metal library
- AMBER: ZN prepin
- Amber: ZN-complex file
- AMBER: ZN-CYS prepin and frcmd file
- AMBER: Zn2+ and Ca2+ ions explicitly treated in MMPB/GB/SA
- AMBER: Zoom
- AMBER: zzfft error for pmemd in Amber 9/Opteron
- AMBER: zzfft issue resolved -thanks!
- AMBER: ´ð¸´: AMBER: pmf input files
- AMBER: ´ð¸´: AMBER: Review.
- AMBER:a problem in parallel compiler
- AMBER:Checkoverlap query
- AMBER:it seems that The SAS in MMPBSA is SES , not SAS. ????
- AMBER:molsurf: molsurf.c:1057: is_buried: Assertion `sarg1 >= 0.0' failed
- AMBER:pls help load peptoid residues in antechamber
- antechamber and FMN
- antechamber bond typing questions
- antechamber failure on FMN
- Antechamber poorly define atom angles of a five ring system whichcauses NH2 and C not to be planar as expected
- antechamber:tutorial
- atom nomination in the PDB file produced by Amber
- AW: AMBER: how to feed dihedral angles of our choice to the linear sequence in amber8
- Confusion re AMBER SMD output
- Distance between two atoms
- FF problem: RG residue minimizes to non-planar structure
- Fluorine and Bromine Parameters in Amber 9
- Force Decomposition for MTS in AMBER 8.
- Fwd: AMBER: How to build N-terminal of alanine : NH2
- Fwd: AMBER: How to calculate the mmpbsa for explicit MD ?
- Fwd: AMBER: LEaP error : unbalanced charge
- Fwd: AMBER: MMPBSA error
- Fwd: AMBER: sander error: rst file crash
- Fwd: Fwd: AMBER: How to calculate the mmpbsa for explicit MD ?
- Fwd: Fwd: AMBER: LEaP error : unbalanced charge
- Fwd: Fwd: AMBER: MMPBSA error
- Fwd: Fwd: Fwd: AMBER: LEaP error : unbalanced charge
- hi & question
- I got the error meassage in testcase of QMMM
- IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031
- installation instructions
- Intel Compiler.
- PMEMD compilation problems
- Problem in compiling sander with MMTSB
- Problems installing antechamber 1.27
- protein simulation using AMBER
- Respgen segemtation fault
- Respgen segemtation fault - debug attempt
- RE£ºAMBER: the problem of mdcrd
- RMSd calculations
- Simulated annealing
- Strange problems with PMEMD on Intel Xeons with Infiniband
- To dac --AMBER: anal: dihedral error
- top2mol2.c scanf format string bug
- trouble stripping waters with ptraj
- Unit of force
Last message date: Sat Dec 30 2006 - 07:20:23 CST
Archived on: Wed Feb 21 2007 - 22:44:15 CST
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