Amber Archive Jul 2010 by subject
- [AMBER] (no subject)
- [AMBER] 1D PMF
- [AMBER] 1D-RISM in AmberTools: atom order in output, a bug?
- [AMBER] 1D-RISM in AmberTools: the reference for ion parameters and LJ parameters
- [AMBER] 3D-RISM disabled?
- [AMBER] 3D-RISM in NAB AmberTools: 2) what is tolerance
- [AMBER] 3D-RISM in NAB AmberTools: what is tolerance and initial guess
- [AMBER] A clear procedure to do WHAM based on the REMD simulations outputs
- [AMBER] about dielectric constant..
- [AMBER] about grid & radial distribution function
- [AMBER] About RAMD
- [AMBER] About the ptraj problem
- [AMBER] adding counterions
- [AMBER] adding ion concentration
- [AMBER] Adding Ions.
- [AMBER] addles
- [AMBER] Align two ligands
- [AMBER] AMBER purchase
- [AMBER] amber tool installing problem
- [AMBER] Amber web page is slow
- [AMBER] amber02pol: sequence: Illegal UNIT named: NHE
- [AMBER] AmberTools citation
- [AMBER] AmberTools installation in Cygwin
- [AMBER] AmberTools installation in Cygwin --- thanks and new errors
- [AMBER] AmberTools1.3 with amber9
- [AMBER] ANALYSES LIGAND EXIT TRAJECTORIES
- [AMBER] analysising trajectory
- [AMBER] antechamber vs. RED
- [AMBER] antechamber vs. REDDB
- [AMBER] Any parameters for Mg2+?
- [AMBER] Are there any GPU clusters that offer compute time?
- [AMBER] atom-type cz ???
- [AMBER] atomic radii of ions
- [AMBER] b-factor
- [AMBER] Calculation of Intramolecular hydrogen bonding using ptraj
- [AMBER] calculation of sasa
- [AMBER] Can I calculate the interaction energy between two connected domains of a protein using mmpbsa.py?
- [AMBER] Can I calculate the interaction energy between two connected domains of a protein?
- [AMBER] Check out my photos on Facebook
- [AMBER] Checking multiple production run
- [AMBER] clustering analysis changes my coordinates
- [AMBER] Combine trajectory files error
- [AMBER] compile ambertools on mac
- [AMBER] compiling amber 10 with mpi
- [AMBER] Compiling failure of Amber 9
- [AMBER] Conformation capture in molecular dynamics
- [AMBER] Constant pH simulation at pH 7
- [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes
- [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes -- thanks and more questions
- [AMBER] Coulson vs. Mulliken, CM1, etc. in antechamber + mopac
- [AMBER] counterions placings
- [AMBER] create a prmtop file without water & ions,
- [AMBER] cumulative patch with two bugfixes for threaded mm_pbsa.pl
- [AMBER] Davies Bouldin Index with DME in ptraj
- [AMBER] dipole moment of binary mixture box
- [AMBER] distance between two residues from their center of mass
- [AMBER] Do I have to keep the Na+ counterions in prmtop and snapshot generation when I do mmGBSA/PBSA calculation?
- [AMBER] dyld: lazy symbol binding failed: Symbol not found: _iconv_open
- [AMBER] energies in amber, namd and gromacs
- [AMBER] Enquiry about NED calculation in AMBER10
- [AMBER] entropy from mass weighted covariance matrix
- [AMBER] error 126 when install AmberTool1.4
- [AMBER] Error Compiling NAB o AMBER Tools 1.2
- [AMBER] error massage in constant pH simulation
- [AMBER] Error report please fix it
- [AMBER] errors of energy decomposition
- [AMBER] external electric field?
- [AMBER] FATAL: Atom .R<LIG 1184>.A<CAA 1> does not have a type.
- [AMBER] file format
- [AMBER] File MAKE_CRD is not found
- [AMBER] fix CM
- [AMBER] For atom: .R<Na+ 1525>.A<Na+ 1> Could not find type: Na+
- [AMBER] force field parameter and resp charge calculation
- [AMBER] Fwd: Error report please fix it
- [AMBER] gbsa for 1 or 2
- [AMBER] general enquiry
- [AMBER] Getting missing force constants for Amber from Gaussian?
- [AMBER] h bond analysis
- [AMBER] H3O+ force field file
- [AMBER] Head-Tail covalently bound substrate and
- [AMBER] How do define phospho-tyrosine-DA linkage?
- [AMBER] How to calculate the radial distribution function of one of the atom(say P) of one residue ( say R1) to the center of the another residue (R2)
- [AMBER] how to create a mixture solvent of hexane and water
- [AMBER] how to develop parameter for organotin
- [AMBER] How to find the angle bond etc parameters used for practicular atom type used in AMBER?
- [AMBER] how to generate porcupine plot
- [AMBER] How to make hexane parameter using antechamber ?
- [AMBER] How to make oligo-peptides using AMBER ?
- [AMBER] how to prepare a system with solvent of ethanol + water ?
- [AMBER] How to prepare the same prmtop from two PDBs for NED analysis?
- [AMBER] How to remove PBC effects?
- [AMBER] hydrogen bond printout
- [AMBER] installing AmberTools 1.4 on AIX
- [AMBER] Invitation to connect on LinkedIn
- [AMBER] Is It Possible to Prevent Center-of-Mass Rotation During MD?
- [AMBER] Issue with preparing pdb, top and crd files via leap for a non-standard residue
- [AMBER] L and D peptides
- [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o
- [AMBER] License
- [AMBER] maintaining temperature scheme
- [AMBER] make test trouble with Amber11
- [AMBER] make test.parallel
- [AMBER] mandatory command lines in MMPBSA.PY
- [AMBER] minimization segmentation fault
- [AMBER] Minor Typo bug.
- [AMBER] Missing BELE for MM in 1 ( residue 1)
- [AMBER] MM-PBSA per residue decompostion
- [AMBER] MM-PBSA/MM-GBSA: mono valent salt
- [AMBER] mm_pbsa.pl in PARALLEL - part 2
- [AMBER] mm_pbsa.pl in PARALLEL - part 3
- [AMBER] mm_pbsa.pl in PARALLEL does not finish
- [AMBER] mmgbsa for ternary system
- [AMBER] mmgbsa tricky output
- [AMBER] mmgbsa tricky output: PART 2
- [AMBER] MMPBSA using counterions
- [AMBER] MMPBSA.py install error
- [AMBER] MMPBSA.py source files
- [AMBER] MMPBSA.PY with two parts receptor
- [AMBER] mpi with openmpi
- [AMBER] mpi with openmpi - SGE error
- [AMBER] mpi with openmpi - with input files
- [AMBER] Mutation of DNA
- [AMBER] NAB problem with a metallic atom
- [AMBER] NAB rdparm seg fault
- [AMBER] NAB: pbc calculations available after all?
- [AMBER] nmode problem with mm_pbsa.pl
- [AMBER] No potential terms in sander output! Check out put files - MMPBSA.py.MPI
- [AMBER] No solvent overlap
- [AMBER] obtain a .pdb file from a .prepin/.frcmod file
- [AMBER] OpenMP programs
- [AMBER] Parallel pmemd.cuda: any preliminary cross-node tests?
- [AMBER] Parallel test times
- [AMBER] Parameters missing after changing topology
- [AMBER] Performance from pmemd.cuda
- [AMBER] Periodic Neighbor Distance
- [AMBER] Permission to post Admin processes?
- [AMBER] please, units of LENNARD_JONES_ACOEF in prmptop?
- [AMBER] PM6 in Amber 11
- [AMBER] pmemd amber10 compilation error
- [AMBER] PMEMD installation error
- [AMBER] PMF from EVB calculations
- [AMBER] POPC parameters
- [AMBER] problem about cyclic peptide
- [AMBER] problem in converting cprestrt to cpin2 file in constant pH md
- [AMBER] problem with 2d-rmsd based clustering
- [AMBER] Problem with pmemd.cuda
- [AMBER] Problem with sander.MPI
- [AMBER] problem with the total charge
- [AMBER] problem with tleap and xleap
- [AMBER] Problems using library file containing multiple residues to make a complex
- [AMBER] problems with NAB and SHIFTS
- [AMBER] protein distance constraints
- [AMBER] ptraj
- [AMBER] ptraj (AT 1.4) hiccups with gzipped trajectory files
- [AMBER] ptraj clustering:*** glibc detected *** /soft/amber11/exe/ptraj: double free or corruption
- [AMBER] ptraj-clustering
- [AMBER] Query regarding Abscissa and their corresponding weights in Thermodynamic Integration
- [AMBER] question about bond command
- [AMBER] Question about increasing the max number of atoms in mopac in antechamber
- [AMBER] Question about sqm in antechamber
- [AMBER] Question about xleap: How to define a linkage between DNA and phosphotyrosine.
- [AMBER] questions of decomposition using mm/gbsa
- [AMBER] Questions with input file in constant pH MD
- [AMBER] radial distribution function
- [AMBER] radius of K+ ions
- [AMBER] random number seed - range
- [AMBER] RDF 3 files and 3 columns
- [AMBER] RDF analysis of glucose made by GLYCAM problem
- [AMBER] Reference of ion parameters employed in parm99
- [AMBER] reference structure
- [AMBER] Regarding Antechamber Tutorial
- [AMBER] regarding IWRAP in Sander
- [AMBER] regarding mmpbsa
- [AMBER] regarding remd
- [AMBER] Relax command for tleap
- [AMBER] Release of the R.E.D.-III.4 tools
- [AMBER] residue wise rmsd, not getting expected results
- [AMBER] residues lacking connect
- [AMBER] RESP "too many charge-group constraints" error
- [AMBER] RESP charges outside Gaussian
- [AMBER] Restrain with PMEMD
- [AMBER] results calculated by mmpbsa.pl and mmpbsa.py
- [AMBER] rfree: Error decoding variable 2 2
- [AMBER] rms command
- [AMBER] same dihedral with different parameter in FRCMOD file
- [AMBER] scee EEL and scnb VDW 1-4
- [AMBER] segmentation fault
- [AMBER] Segmentation fault in MMPBSA.PY with two parts receptor
- [AMBER] Segmentation fault with translate command
- [AMBER] Should I define drug intercalation site of a DNA as internal (DT/DA) or terminal (DT3/DA5) unit ?
- [AMBER] sign me off please~
- [AMBER] simulate large molecules with implicit water model (GB)
- [AMBER] Simulation cell reduction
- [AMBER] simulation runs very slow..
- [AMBER] simulations in urea
- [AMBER] Solvation in water
- [AMBER] source code to calculate electrostatic interaction in amber6
- [AMBER] Steered MD calc
- [AMBER] step 0 of minimization ?
- [AMBER] test of parallel NAB and PTRAJ
- [AMBER] Thank you Jason, Bill and Oliver
- [AMBER] The atom number exceeds the MAXATOM, reallocate memory Segmentation fault (core dumped)
- [AMBER] The atom number exceeds the MAXATOM, reallocate memory Segmentation fault (core dumped) --- thank you and more questions!
- [AMBER] The system size limitations for Tesla C2050 ?
- [AMBER] TI calculation using softcore potentials. simultaneous density and temperature equilibration
- [AMBER] TIP4P question
- [AMBER] tleap and sander minimization
- [AMBER] Units for mass weighted covariance matrix in ptraj
- [AMBER] very high and unstable RMSD
- [AMBER] vlimit exceeded after 10ns MD
- [AMBER] vlimit exceeded for step
- [AMBER] vlimit exceeding situtaion with ntt option
- [AMBER] Warning: Input error! "nmode_igb=1" is an invalid option.
- [AMBER] WARNING: Local coordinate 1 differs from partner coordinate 1 !
- [AMBER] WARNING: Local coordinate 382 differs from partner coordinate 382 !
- [AMBER] website down
- [AMBER] What ab initio methods can be choose for QM/MM package in AMBER10?
- [AMBER] What is the command to add two tails for a new residue in xleap?
- [AMBER] What is the max atom can be run by addles in amber10?
- [AMBER] What is the way to change from MMPBSA+GBSA to MMGBSA only input file.
- [AMBER] Where can I find a tutorial/manual on the IED in VMD for visualizing PCA data from ABMER?
- [AMBER] Which one, ESP calculation?
- [AMBER] Workaround for gfortran-4.1.2?
- [AMBER] xleap error
- ptraj clustering:*** glibc detected *** /soft/amber11/exe/ptraj: double free or corruption]
- Last message date: Sat Jul 31 2010 - 17:30:03 PDT
- Archived on: Wed Oct 02 2024 - 05:54:06 PDT