Amber Archive Jun 2009: by date

Monday, 1 June 2009
- [AMBER] sleap and delete FyD
- Re: [AMBER] Choice of force field Carlos Simmerling
- RE: [AMBER] QQD psuedoatom restraints Titus, Jamie (bairdje)
- [AMBER] converting vibrational frequency aneesh cna
- Re: [AMBER] converting vibrational frequency David A. Case
- [AMBER] atom number exceeds the MAXATOM when running antechamber xueqin pang
- Re: [AMBER] MM-PBSA nmode statistics Dmitry Osolodkin
- [AMBER] different comformations to choose for RESP xueqin pang
- Re: [AMBER] different comformations to choose for RESP FyD
- Re: [AMBER] converting vibrational frequency aneesh cna
- RE: [AMBER] MM-PBSA nmode statistics Ray Luo
- Re: [AMBER] makeDIST_RST: no map function for ambiguous restraint Peter Varnai
- Re: [AMBER] ask for parm99MOD Carlos Simmerling
- [AMBER] minimization to reduce covalent deviation Peter Varnai
- RE: [AMBER] ask for parm99MOD xiaoqin huang
- [AMBER] how to choose different comformations for RESP xueqin pang
- Re: [AMBER] how to choose different comformations for RESP cgji
- [AMBER] MMPBSA and mm_pbsa_statistics.pl error john smith
Tuesday, 2 June 2009
- [AMBER] how to add ions bharat lakhani
- [AMBER] Atom names Rose Tamil
- Re: [AMBER] Atom names Carlos Simmerling
- Re: [AMBER] Atom names David A. Case
- Re: [AMBER] Atom names Rose Tamil
- [AMBER] help with parameters for ions rebeca
- Re: [AMBER] minimization to reduce covalent deviation David A. Case
- [AMBER] Error in MM PBSA Vikas Sharma
- Re: [AMBER] help with parameters for ions David A. Case
- Re: [AMBER] Error in MM PBSA David A. Case
- Re: [AMBER] J coupling constant calculation Gustavo Seabra
- 回复： [AMBER] Error in MM PBSA 廖青华
- Re: 回复： [AMBER] Error in MM PBSA David A. Case
- Re: [AMBER] Targeted MD and QM/MM Gustavo Seabra
- Re: [AMBER] Can we use GROMACS or NAMD for MD, and then use MM-PBSA to culculate binding energy Gustavo Seabra
- Re: [AMBER] Choice of force feild Gustavo Seabra
- Re: [AMBER] atom number exceeds the MAXATOM when running antechamber Gustavo Seabra
- Re: [AMBER] help with parameters for ions rebeca
- Re: [AMBER] create a simulation box Gustavo Seabra
- Re: [AMBER] help with parameters for ions InSuk Joung
- Re: [AMBER] help with parameters for ions rebeca
- Re: [AMBER] help with parameters for ions InSuk Joung
- Fwd: Re: [AMBER] help with parameters for ions rebeca
- Re: [AMBER] Can we use GROMACS or NAMD for MD, and then use MM-PBSA to culculate binding energy Marc Baaden
- [AMBER] PARMSCAN alegil.fq.uh.cu
- Re: [AMBER] Targeted MD and QM/MM Gabriel Urquiza
- [AMBER] PARMSCAN alegil.fq.uh.cu
- [AMBER] preparation of two solutes of organic molecules in a simulation box Workalemhu Berhanu
- Re: [AMBER] MMPBSA and mm_pbsa_statistics.pl error Ray Luo
- [AMBER] addions Shubhra Gupta
- Re: [AMBER] Error in MM PBSA Vikas Sharma
- Re: [AMBER] Error in MM PBSA Vikas Sharma
- Re: [AMBER] Error in MM PBSA Vikas Sharma
- [AMBER] Distance restraints between groups of atoms Germain Vallverdu
Wednesday, 3 June 2009
- [AMBER] use of random seed in multiple runs Andrew Voronkov
- Re: [AMBER] use of random seed in multiple runs Carlos Simmerling
- [AMBER] only ff94 and ff99 for GBSA? Andrew Voronkov
- Re: [AMBER] only ff94 and ff99 for GBSA? Carlos Simmerling
- [AMBER] Re: addions Shubhra Gupta
- Re: [AMBER] Error in MM PBSA David A. Case
- Re: [AMBER] only ff94 and ff99 for GBSA? Andrew Voronkov
- Re: [AMBER] only ff94 and ff99 for GBSA? David A. Case
- Re: [AMBER] Distance restraints between groups of atoms David A. Case
- [AMBER] NO output when running espgen? xueqin pang
- Re: [AMBER] Re: addions nicholus bhattacharjee
- Re: [AMBER] Can we use GROMACS or NAMD for MD, and then use MM-PBSA to culculate binding energy jacky zhao
- Re: [AMBER] use of random seed in multiple runs Gustavo Seabra
- [AMBER] Pentavalent Phosphorous and Antechamber Peterson, Matthew W.
- [AMBER] AMBER10: error message mdfil flag..... Catein Catherine
- [AMBER] Re: addions Peter Gannett
- Re: [AMBER] Error in MM PBSA Vikas Sharma
- Re: [AMBER] AMBER10: error message mdfil flag..... David A. Case
- [AMBER] spc.itp for the Amber force field rebeca
- Re: [AMBER] Distance restraints between groups of atoms Germain Vallverdu
- Re: [AMBER] Atom names Rose Tamil
- Re: [AMBER] spc.itp for the Amber force field Alan
- [AMBER] problems with EP of TIP4PEW rebeca
- Re: [AMBER] Atom names David A. Case
- Re: [AMBER] problems with EP of TIP4PEW David A. Case
- Re: [AMBER] Distance restraints between groups of atoms David A. Case
- Re: [AMBER] Pentavalent Phosphorous and Antechamber David A. Case
- Re: [AMBER] hbond_DNAtraj Jianyin Shao
- Re: [AMBER] use of random seed in multiple runs Andrew Voronkov
- [AMBER] creating bond Jorgen Simonsen
- Re: [AMBER] creating bond David A. Case
- Re: [AMBER] problems with EP of TIP4PEW rebeca
- Re: [AMBER] creating bond Bill Ross
- Re: [AMBER] use of random seed in multiple runs Andrew Voronkov
- Re: [AMBER] creating bond Jorgen Simonsen
- [AMBER] ptraj image in non-orthorhombic cell Joanna Panecka
- Re: [AMBER] Atom names Rose Tamil
- Re: [AMBER] creating bond Bill Ross
- Re: [AMBER] use of random seed in multiple runs Gustavo Seabra
- Re: [AMBER] use of random seed in multiple runs Robert Duke
- Re: [AMBER] Pentavalent Phosphorous and Antechamber Shubhra Gupta
- [AMBER] AMBER 10: sleap diff errors? Catein Catherine
- [AMBER] no output when running Antechamber(espgen) xueqin pang
- Re: [AMBER] Pentavalent Phosphorous and Antechamber FyD
Thursday, 4 June 2009
- [AMBER] how to add water for membrane, in Z direction only or xyz xueqin pang
- [AMBER] Binding Energy Vikas Sharma
- Re: [AMBER] use of random seed in multiple runs Jifeng Wang
- Re: [AMBER] ligand QM/semi-empirical coords optmisation Alan
- Re: [AMBER] use of random seed in multiple runs Robert Duke
- Re: [AMBER] use of random seed in multiple runs Jifeng Wang
- [AMBER] Error in MM PBSA Vikas Sharma
- Re: [AMBER] ligand QM/semi-empirical coords optmisation David A. Case
- Re: [AMBER] use of random seed in multiple runs Marek Maly
- [AMBER] mol2 file to amber pdb file format balaji nagarajan
- Re: [AMBER] rescaling velocities Carlos Simmerling
- [AMBER] rescaling velocities abi ghanem
- Re: [AMBER] mol2 file to amber pdb file format David A. Case
- Re: [AMBER] use of random seed in multiple runs Robert Duke
- Re: [AMBER] ligand QM/semi-empirical coords optmisation Alan
- Re: [AMBER] use of random seed in multiple runs Marek Maly
- Re: [AMBER] AMBER 10: sleap diff errors? David A. Case
- Re: [AMBER] use of random seed in multiple runs Carlos Simmerling
- Re: [AMBER] use of random seed in multiple runs Marek Maly
- Re: [AMBER] Error in MM PBSA Ray Luo
- [AMBER] ptraj_hbond_problem balaji nagarajan
- [AMBER] atom type Taufik Al-Sarraj
- Re: [AMBER] Re: addions Shubhra Gupta
- Re: [AMBER] ptraj_hbond_problem Thomas Cheatham
Friday, 5 June 2009
- [AMBER] Warning: No sp2 improper torsion term for Alan
- Re: [AMBER] atom type David A. Case
- Re: [AMBER] use of random seed in multiple runs Gustavo Seabra
- Re: [AMBER] use of random seed in multiple runs Gustavo Seabra
- Re: [AMBER] use of random seed in multiple runs Marek Maly
- Re: [AMBER] atom type Taufik Al-Sarraj
- RE: [AMBER] Warning: No sp2 improper torsion term for Ross Walker
- Re: [AMBER] use of random seed in multiple runs Robert Duke
- Re: [AMBER] use of random seed in multiple runs Robert Duke
- Re: [AMBER] ligand QM/semi-empirical coords optmisation Junmei Wang
- Re: [AMBER] use of random seed in multiple runs Gustavo Seabra
- [AMBER] parameter for dihedral angle Jorgen Simonsen
- Re: [AMBER] use of random seed in multiple runs Naser Alijabbari
- Re: [AMBER] use of random seed in multiple runs Robert Duke
- Re: [AMBER] atom type Taufik Al-Sarraj
- [AMBER] Proper ISTRNG value ? Marek Maly
- Re: [AMBER] ligand QM/semi-empirical coords optmisation Francesco Pietra
- Re: [AMBER] use of random seed in multiple runs Gustavo Seabra
- Re: [AMBER] use of random seed in multiple runs Marek Maly
- Re: [AMBER] parameter for dihedral angle David A. Case
- [AMBER] Computational Alanine Scanning using mm_pbsa, any tutorial for amber9 or amber 10 version? Haizhen Zhong
- Re: [AMBER] parameter for dihedral angle raja pandian
Saturday, 6 June 2009
- Re: [AMBER] Error in MM PBSA Vikas Sharma
- Re: [AMBER] parameter for dihedral angle David A. Case
- Re: [AMBER] Error in MM PBSA Ray Luo
- [AMBER] average torsional energy Francesco Pietra
- [AMBER] MaxRad ? Marek Maly
Sunday, 7 June 2009
- Re: [AMBER] average torsional energy Adrian Roitberg
- [AMBER] Fwd: average torsional energy Francesco Pietra
- Re: [AMBER] average torsional energy Carlos Simmerling
- Re: [AMBER] Error in MM PBSA Vikas Sharma
- [AMBER] POL3 Hemant Kumar
- Re: [AMBER] Error in MM PBSA Ray Luo
- [AMBER] vs_vikassharma.yahoo.co.in has sent you a private message Vikas S
- [AMBER] How to calculate the distance of CA of all residues in the trajectory Thomas Leonard
- RE: [AMBER] parameter for dihedral angle Catein Catherine
- [AMBER] Error message? INFO: Old style inpcrd file read Catein Catherine
- [AMBER] What is the parallel efficiency of amber10 Catein Catherine
- Re: [AMBER] Error message? INFO: Old style inpcrd file read Robert Duke
- RE: [AMBER] Error message? INFO: Old style inpcrd file read Catein Catherine
- Re: [AMBER] What is the parallel efficiency of amber10 Tom Joseph
Monday, 8 June 2009
- Re: [AMBER] average torsional energy Karl Kirschner
- Re: [AMBER] average torsional energy Francesco Pietra
- [AMBER] Max filename length in Sander? Paul Mortenson
- [AMBER] (no subject) Vishal Maingi
- Re: [AMBER] (no subject) Karl Kirschner
- [AMBER] Lost mail Robert Duke
- Re: [AMBER] What is the parallel efficiency of amber10 David A. Case
- Re: [AMBER] Max filename length in Sander? David A. Case
- Re: [AMBER] Max filename length in Sander? David A. Case
- [AMBER] problem with creation of prmtop and prmcrd files moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] What is the parallel efficiency of amber10 Gustavo Seabra
- [AMBER] Problem with modified trna[Fwd: problem with creation of prmtop and prmcrd files] moitrayee.mbu.iisc.ernet.in
- [AMBER] sander error Beale, John
- [AMBER] Problem with modified trna[Fwd: problem with creation of prmtop and prmcrd files]] moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] Warning: No sp2 improper torsion term for Alan
- [AMBER] Can we define +1 or -1 charge for an organic drug using GAFF? Catein Catherine
- Re: [AMBER] Can we define +1 or -1 charge for an organic drug using GAFF? David A. Case
- Re: [AMBER] (no subject) FyD
- Re: [AMBER] Max filename length in Sander? Robert Duke
- Re: [AMBER] Error in MM PBSA Vikas Sharma
- Re: [AMBER] Error in MM PBSA Ray Luo
- [AMBER] Unknown residue: MOL number: 30 type: Terminal/last Workalemhu Berhanu
- [AMBER] mm_pbsa_statistics-CALC DELTA parameter ? Marek Maly
- [AMBER] Strange contacts with water molecules Jordan MONNET
- RE: [AMBER] sander error Ross Walker
- RE: [AMBER] Strange contacts with water molecules Ross Walker
- Re: [AMBER] sander error Robert Duke
- [AMBER] PDMED Catein Catherine
- RE: [AMBER] PDMED Ross Walker
- RE: [AMBER] PDMED Catein Catherine
- [AMBER] Error in MM PBSA (vertex atom mismatch) Vikas Sharma
- RE: [AMBER] PDMED Ross Walker
- [AMBER] ptraj quasiharmonic analysis Neha Gandhi
Tuesday, 9 June 2009
- Re: [AMBER] ptraj quasiharmonic analysis Hannes Loeffler
- Re: [AMBER] Distance restraints between groups of atoms Germain Vallverdu
- [AMBER] (no subject) david.lisgarten.canterbury.ac.uk
- [AMBER] SOS - too high binding energy Marek Maly
- Re: [AMBER] Distance restraints between groups of atoms David A. Case
- Re: [AMBER] (no subject) David A. Case
- [AMBER] unit of charge in prep files moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] Unknown residue: MOL number: 30 type: Terminal/last David A. Case
- [AMBER] Question of about MM-PBSA and mm_pbsa_createinput.pm script Samuel Genheden
- Re: [AMBER] unit of charge in prep files David A. Case
- Re: [AMBER] Question of about MM-PBSA and mm_pbsa_createinput.pm script David A. Case
- [AMBER] Vertex atom mismatch in Amber Vikas Sharma
- RE: [AMBER] (no subject) david.lisgarten.canterbury.ac.uk
- [AMBER] DNA as well as protein distorted during MD run in sander Jayalakshmi Sridhar
- Re: [AMBER] DNA as well as protein distorted during MD run in sander Carlos Simmerling
- RE: [AMBER] Max filename length in Sander? Paul Mortenson
- Re: [AMBER] Max filename length in Sander? Robert Duke
- Re: [AMBER] DNA as well as protein distorted during MD run in sander Jayalakshmi Sridhar
- Re: [AMBER] DNA as well as protein distorted during MD run in sander Carlos Simmerling
- RE: [AMBER] DNA as well as protein distorted during MD run in sander Jesse Dylan Ziebarth (jziebrth)
- Re: [AMBER] DNA as well as protein distorted during MD run in sander Carlos Simmerling
- Re: [AMBER] Strange contacts with water molecules Jordan MONNET
- Re: [AMBER] DNA as well as protein distorted during MD run in sander Jayalakshmi Sridhar
- [AMBER] Improper dihedrals between residues? Ben Roberts
- Re: [AMBER] Improper dihedrals between residues? Carlos Simmerling
- Re: [AMBER] Improper dihedrals between residues? David A. Case
- Re: [AMBER] Improper dihedrals between residues? Carlos Simmerling
- Re: [AMBER] Improper dihedrals between residues? Bill Ross
- Re: [AMBER] Improper dihedrals between residues? Ben Roberts
- [AMBER] POL3 & SHAKE Hemant Gangwar
- Re: [AMBER] Improper dihedrals between residues? Bill Ross
- Re: [AMBER] unit of charge in prep files moitrayee.mbu.iisc.ernet.in
- [AMBER] MM PBSA ( Vertex atom mismatch in Amber) Vikas Sharma
- [AMBER] unit of force constant aneesh cna
Wednesday, 10 June 2009
- [AMBER] GAFF and solvents.lib error Vishal Maingi
- [AMBER] Thermodynamic parameters in mm_PBSA - NAB ? Marek Maly
- [AMBER] partial charges from AM1-BCC and RESP differ a lot xueqin pang
- [AMBER] force.f routine Brad Dickson
- [AMBER] Completed installation of AmberTools, version 1.1 Alan
- [AMBER] Error in AMBER ( Vertex atom mismatch in Amber) Vikas Sharma
- Re: [AMBER] force.f routine David A. Case
- Re: [AMBER] Completed installation of AmberTools, version 1.1 David A. Case
- [AMBER] question lev kantorovich
- [AMBER] compiling amber10 with mac intel, ifort/icc and mpi Alan
- [AMBER] RNA and polarizable force field Abhishek Singh
- Re: [AMBER] compiling amber10 with mac intel, ifort/icc and mpi David A. Case
- [AMBER] glycopeptide Parametrization guardiani.fi.infn.it
- [AMBER] GAFF atom type question Cen Gao
- [AMBER] radial distribution without normalization CHAMI F.
- Re: [AMBER] GAFF and solvents.lib error David A. Case
- [AMBER] ptraj amber 10 file. Catein Catherine
- Re: [AMBER] Thermodynamic parameters in mm_PBSA - NAB ? David A. Case
- Re: [AMBER] compiling amber10 with mac intel, ifort/icc and mpi Alan
- Re: [AMBER] compiling amber10 with mac intel, ifort/icc and mpi David A. Case
- [AMBER] entangle-less building Vishal Maingi
- [AMBER] Generating LeAP file for helix containing non-standard amino acid Brothers, Michael Charles
- Re: [AMBER] POL3 & SHAKE David A. Case
- Re: [AMBER] Generating LeAP file for helix containing non-standard amino acid David A. Case
- Re: [AMBER] Generating LeAP file for helix containing non-standard amino acid David A. Case
- RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid Brothers, Michael Charles
- Re: [AMBER] Thermodynamic parameters in mm_PBSA - NAB ? Marek Maly
- Re: [AMBER] SOS - too high binding energy Marek Maly
- Re: [AMBER] glycopeptide Parametrization Ahammadunny Pathiaseril
- [AMBER] input coordinates for vdW transition step in Amber 10 TI Jodi Hadden
- Re: [AMBER] radial distribution without normalization Thomas Cheatham
- Re: [AMBER] entangle-less building Bill Ross
- [AMBER] Constant pH simulation Rukman Hertadi
- Re: [AMBER] input coordinates for vdW transition step in Amber 10 TI Tom Joseph
- Re: [AMBER] Constant pH simulation Tom Joseph
- Re: [AMBER] problem with creation of prmtop and prmcrd files Tom Joseph
- RE: [AMBER] question Ross Walker
- [AMBER] Vertex atom mismatch in Amber Vikas Sharma
- Re: [AMBER] Generating LeAP file for helix containing non-standard amino acid FyD
Thursday, 11 June 2009
- [AMBER] zinc coordination of benzimidazole Aust, Susanne
- RE: [AMBER] (no subject) david.lisgarten.canterbury.ac.uk
- Re: [AMBER] input coordinates for vdW transition step in Amber 10 TI Ye MEI
- Re: [AMBER] zinc coordination of benzimidazole Urszula Uciechowska
- [AMBER] ptraj "image" "center" commands Catein Catherine
- Re: [AMBER] input coordinates for vdW transition step in Amber 10 TI steinbrt.rci.rutgers.edu
- Re: [AMBER] compiling amber10 with mac intel, ifort/icc and mpi Alan
- Re: [AMBER] (no subject) David A. Case
- [AMBER] NOE Beale, John
- Re: [AMBER] compiling amber10 with mac intel, ifort/icc and mpi David Watson
- [AMBER] GAFF atom type question Cen Gao
- [AMBER] Copper semiempirical parameters Jacopo Sgrignani
- RE: [AMBER] ptraj "image" "center" commands Ross Walker
- [AMBER] PRINCIPAL QUESTION Marek Maly
- RE: [AMBER] GAFF atom type question Ross Walker
- RE: [AMBER] Copper semiempirical parameters Ross Walker
- [AMBER] setBox truncated octahedron Myunggi Yi
- Re: [AMBER] NOE David A. Case
- Re: [AMBER] partial charges from AM1-BCC and RESP differ a lot FyD
- Re: [AMBER] GAFF atom type question Cen Gao
- AW: [AMBER] zinc coordination of benzimidazole Aust, Susanne
Friday, 12 June 2009
- Re: [AMBER] glycopeptide Parametrization FyD
- [AMBER] MM PBSA ERROR Vikas Sharma
- [AMBER] Is the result of sander same as that of pmemd? Catein Catherine
- Re: [AMBER] glycopeptide Parametrization guardiani.fi.infn.it
- Re: [AMBER] Is the result of sander same as that of pmemd? Robert Duke
- [AMBER] Residues KIRTANA S
- Re: [AMBER] Residues FyD
- Re: [AMBER] glycopeptide Parametrization Karl Kirschner
- Re: [AMBER] Residues KIRTANA S
- Re: [AMBER] Residues FyD
- [AMBER] help KIRTANA S
- [AMBER] dipole printing Hemant Kumar
- RE: [AMBER] help Ross Walker
- RE: [AMBER] glycopeptide Parametrization Ross Walker
- RE: [AMBER] dipole printing Ross Walker
- RE: [AMBER] QQD psuedoatom restraints Titus, Jamie (bairdje)
- RE: [AMBER] dipole printing Hemant Kumar
- Re: [AMBER] Residues KIRTANA S
- Re: [AMBER] Residues Bill Ross
- [AMBER] Re: Residues KIRTANA S
- RE: [AMBER] Is the result of sander same as that of pmemd? Catein Catherine
Saturday, 13 June 2009
- [AMBER] AMBER ERROR Vikas Sharma
- RE: [AMBER] glycopeptide Parametrization FyD
- [AMBER] Re: [Contact q4md] qurey reagarding RED Server FyD
- [AMBER] too high in binding energy (MM-PBSA) Maryam Hamzehee
- 回复： [AMBER] too high in binding energy (MM-PBSA) 廖青华
- Re: 回复： [AMBER] too high in binding energy (MM-PBSA) Maryam Hamzehee
- 回复：回复： [AMBER] too high in binding energy (MM-PBSA) 廖青华
- RE: [AMBER] Is the result of sander same as that of pmemd? Ross Walker
- Re: 回复：回复： [AMBER] too high in binding energy (MM-PBSA) Maryam Hamzehee
- Re: 回复：回复： [AMBER] too high in binding energy (MM-PBSA) Maryam Hamzehee
- Re: 回复：回复： [AMBER] too high in binding energy (MM-PBSA) Maryam Hamzehee
- Re: 回复：回复： [AMBER] too high in binding energy (MM-PBSA) Ilyas Yildirim
- Re: [AMBER] compiling amber10 with mac intel, ifort/icc and mpi Alan
- Re: [AMBER] Residues KIRTANA S
- 回复：回复：回复： [AMBER] too high in binding energy (MM-PBSA) 廖青华
Sunday, 14 June 2009
- Re: [AMBER] Residues FyD
- [AMBER] PLEASE HELP - PDB Modification s_bill36.yahoo.co.uk
- Re: [AMBER] PLEASE HELP - PDB Modification Tom Joseph
- Re: [AMBER] GAFF atom type question Cen Gao
- Re: [AMBER] Residues FyD
Monday, 15 June 2009
- [AMBER] parallel error 廖青华
- [AMBER] covalent interaction 廖青华
- Re: 回复：回复：回复： [AMBER] too high in binding energy (MM-PBSA) Maryam Hamzehee
- [AMBER] Are ntrp=1000, ntwx=1000, ntwr=500 reasonable for long MD simulations? Catein Catherine
- [AMBER] total charge for NPRO in ff03ua Edyta Malolepsza
- 回复：回复：回复：回复： [AMBER] too high in binding energy (MM-PBSA) 廖青华
- Re: [AMBER] parallel error Tom Joseph
- Re: [AMBER] QQD psuedoatom restraints David A. Case
- 回复： [AMBER] parallel error 廖青华
- Re: 回复： [AMBER] parallel error Tom Joseph
- [AMBER] to unsubscribe email Urszula Uciechowska
- [AMBER] Antechamber am1bcc questions gilbert.bluemarble.net
- 回复：回复： [AMBER] parallel error 廖青华
- Re: 回复：回复： [AMBER] parallel error Tom Joseph
- 回复：回复：回复： [AMBER] parallel error 廖青华
- Re: 回复：回复：回复： [AMBER] parallel error Tom Joseph
- 回复：回复：回复：回复： [AMBER] parallel error 廖青华
- [AMBER] to check basepair in ptraj balaji nagarajan
- RE: [AMBER] Are ntrp=1000, ntwx=1000, ntwr=500 reasonable for long MD simulations? Ross Walker
- [AMBER] Histidine, which form? s_bill36.yahoo.co.uk
- Re: [AMBER] Histidine, which form? Carlos Simmerling
- RE: [AMBER] Histidine, which form? Ross Walker
- [AMBER] pKa data base.... s. Bill
- Re: [AMBER] Histidine, which form? s. Bill
- RE: [AMBER] Histidine, which form? Ross Walker
- Re: [AMBER] Histidine, which form? M. L. Dodson
- RE: [AMBER] to unsubscribe email Ross Walker
- [AMBER] Need help with nab code to access the m_prm struct in a molecule M. L. Dodson
- [AMBER] Re: connect KIRTANA S
- Re: [AMBER] Re: connect Bill Ross
- RE: [AMBER] total charge for NPRO in ff03ua Jun Wang
- RE: [AMBER] Re: connect Ross Walker
- [AMBER] Distance-covariance and PCA questions... Cihan Aydin
- [AMBER] problem in pressure equillibration wong105.llnl.gov
Tuesday, 16 June 2009
- RE:Re: [AMBER] partial charges from AM1-BCC and RESP differ a lot xueqin pang
- Re: [AMBER] total charge for NPRO in ff03ua Edyta Malolepsza
- Re: [AMBER] problem in pressure equillibration David A. Case
- [AMBER] Fix the local structure as a rigid body Yunjie Zhao
- Re: [AMBER] Fix the local structure as a rigid body Carlos Simmerling
- Re: [AMBER] Fix the local structure as a rigid body Yunjie Zhao
- Re: [AMBER] Fix the local structure as a rigid body Carlos Simmerling
- [AMBER] Sander imin=5 option Paul Mortenson
- Re: [AMBER] Sander imin=5 option Carlos Simmerling
- RE: [AMBER] Sander imin=5 option Paul Mortenson
- [AMBER] MM decomp energy - zero values for Eele, Evdw Thomas Lake
- Re: [AMBER] Fix the local structure as a rigid body David A. Case
- [AMBER] connecting residues KIRTANA S
- Re: [AMBER] Distance-covariance and PCA questions... Bill Ross
- Re: [AMBER] connecting residues Bill Ross
- Re: [AMBER] connecting residues Bill Ross
- [AMBER] Seg-fault when creating residue Valla Fatemi
- [AMBER] improper torsion problem Youn Kyeung Lee
- RE:Re: [AMBER] partial charges from AM1-BCC and RESP differ a lot FyD
- [AMBER] GLYCAM: warnings by writing topology Sergey Samsonov
- [AMBER] How to calculate SASA in vmd Mannan
Wednesday, 17 June 2009
- [AMBER] to unsubscribe email backy
- Re: [AMBER] GLYCAM: warnings by writing topology FyD
- Re: [AMBER] Distance-covariance and PCA questions... Hannes Loeffler
- Re: [AMBER] improper torsion problem Bill Ross
- Re: [AMBER] Seg-fault when creating residue Bill Ross
- Re: [AMBER] GLYCAM: warnings by writing topology Sergey Samsonov
- Re: [AMBER] GLYCAM: warnings by writing topology Bill Ross
- RE: [AMBER] to unsubscribe email Ross Walker
- Re: [AMBER] GLYCAM: warnings by writing topology Sergey Samsonov
- Re: [AMBER] GLYCAM: warnings by writing topology Sergey Samsonov
- [AMBER] vlimit in TI with soft core potential Ye MEI
- Re: [AMBER] to unsubscribe email backy
- Re: [AMBER] GLYCAM: warnings by writing topology Karl Kirschner
- Re: [AMBER] vlimit in TI with soft core potential steinbrt.rci.rutgers.edu
- Re: [AMBER] GLYCAM: warnings by writing topology Sergey Samsonov
- Re: [AMBER] vlimit in TI with soft core potential Ye MEI
- Re: [AMBER] GLYCAM: warnings by writing topology Shubhra Gupta
- [AMBER] Antechamber: stuck at bondtype Jack Shultz
- Re: [AMBER] Antechamber: stuck at bondtype David A. Case
- Re: [AMBER] Antechamber: stuck at bondtype Ye MEI
- [AMBER] bond length energy Thomas Lake
- [AMBER] Specifying improper dihedrals Ben Roberts
- Re: [AMBER] GLYCAM: warnings by writing topology FyD
- Re: [AMBER] Strange contacts with water molecules Jordan MONNET
- Re: [AMBER] Specifying improper dihedrals Mark Williamson
- Re: [AMBER] bond length energy Mark Williamson
- Re: [AMBER] GLYCAM: warnings by writing topology Bill Ross
- [AMBER] Re: Seg-fault when creating residue Valla Fatemi
- Re: [AMBER] Specifying improper dihedrals Bill Ross
- Re: [AMBER] Specifying improper dihedrals David A. Case
- [AMBER] Coarse grained MD in AMBER ? Siddharth Rastogi
- Re: [AMBER] Coarse grained MD in AMBER ? Lili Peng
- Re: [AMBER] Specifying improper dihedrals Ben Roberts
- Re: [AMBER] Specifying improper dihedrals Ben Roberts
- Re: [AMBER] Specifying improper dihedrals Bill Ross
- [AMBER] where to I get the parameters for Mg divalent ion Mannan
Thursday, 18 June 2009
- [AMBER] force units Brad Dickson
- [AMBER] Re: force units Brad Dickson
- [AMBER] Improper dihedrals from .off and .lib files Johan Sund
- Re: [AMBER] Improper dihedrals from .off and .lib files David A. Case
- Re: [AMBER] Re: force units David A. Case
- [AMBER] guntheyp.aston.ac.uk
- Re: [AMBER] Raja Pandian
- [AMBER] how to create prmtop and inpcrd files for covalent neutral phenylalanine Madhurima Jana
- Re: [AMBER] GLYCAM: warnings by writing topology Sergey Samsonov
- [AMBER] Sulfates parameterization for GAGs in GLYCAM_06 Sergey Samsonov
- [AMBER] ptraj correlation Catein Catherine
- RE: [AMBER] Re: force units Catein Catherine
- [AMBER] Dyndom Chunliyan
- RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid Brothers, Michael Charles
- [AMBER] Fix Residue continued... Vishal Maingi
- Re: [AMBER] Fix Residue continued... Carlos Simmerling
- RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid FyD
- Re: [AMBER] Residues KIRTANA S
- [AMBER] residue KIRTANA S
- [AMBER] Re: R.E.D. error message FyD
- Re: [AMBER] Residues FyD
- RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid Brothers, Michael Charles
- Re: [AMBER] Residues Bill Ross
- Re: [AMBER] Residues Roman Osman
- [AMBER] Postdoc position in biomolecular simulation Ivaylo, Ivanov
- [AMBER] From DLG to Antechamber Jack Shultz
- Re: [AMBER] where to I get the parameters for Mg divalent ion Tom Joseph
- RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid FyD
- [AMBER] Force field parameter for Unionized Phenylalanine HOOC-CH(NH2)-CH2-C6H5 Madhurima Jana
Friday, 19 June 2009
- [AMBER] 2 restraints with different force constants Aust, Susanne
- Re: [AMBER] Force field parameter for Unionized Phenylalanine HOOC-CH(NH2)-CH2-C6H5 FyD
- Re: [AMBER] From DLG to Antechamber FyD
- Re: [AMBER] bond length energy Karl Kirschner
- Re: [AMBER] 2 restraints with different force constants David A. Case
- AW: [AMBER] 2 restraints with different force constants Aust, Susanne
- [AMBER] methyl group at the N-terminal Francesca Poletti
- Re: [AMBER] 2 restraints with different force constants David A. Case
- Re: [AMBER] methyl group at the N-terminal FyD
- Re: [AMBER] From DLG to Antechamber Jack Shultz
- AW: [AMBER] 2 restraints with different force constants Aust, Susanne
- Re: [AMBER] From DLG to Antechamber gilbert.bluemarble.net
- Re: [AMBER] From DLG to Antechamber Jack Shultz
- [AMBER] Re: force units Brad Dickson
- Re: [AMBER] From DLG to Antechamber gilbert.bluemarble.net
- Re: [AMBER] From DLG to Antechamber Jack Shultz
- Re: [AMBER] From DLG to Antechamber Jack Shultz
- [AMBER] Re: residue KIRTANA S
- Re: [AMBER] From DLG to Antechamber FyD
- RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid Brothers, Michael Charles
- [AMBER] RED Geometry Calculation Error Brothers, Michael Charles
- Re: [AMBER] RED Geometry Calculation Error FyD
- [AMBER] atom type no recognize - xleap version 10 but fine in v 9 Peter Gannett
- RE: [AMBER] RED Geometry Calculation Error Brothers, Michael Charles
- [AMBER] PMEMD compilation manoj singh
- [AMBER] Hard limit in Amber10? Yang, Ping
- RE: [AMBER] RED Geometry Calculation Error FyD
Saturday, 20 June 2009
- RE: [AMBER] PMEMD compilation Ross Walker
- RE: [AMBER] Hard limit in Amber10? Ross Walker
- Re: [AMBER] atom type no recognize - xleap version 10 but fine in v 9 case
- R: [AMBER] Amber10 Parallel Installation sgrignani.cerm.unifi.it
- Re: [AMBER] Amber10 Parallel Installation case
- RE: [AMBER] Hard limit in Amber10? Yang, Ping
- Re: [AMBER] PMEMD compilation manoj singh
- RE: [AMBER] PMEMD compilation Ross Walker
- Re: [AMBER] PMEMD compilation manoj singh
- Re: [AMBER] PMEMD compilation manoj singh
- RE: [AMBER] PMEMD compilation Ross Walker
- [AMBER] Your private message from Vikas is about to expire Vikas S
Sunday, 21 June 2009
- [AMBER] Reference Correction Mahmoud A. A. Ibrahim
- [AMBER] reclaiming space from amber10 installation Alan
- [AMBER] parameters Fe4S4 cluster KIRTANA S
Monday, 22 June 2009
- [AMBER] PTRAJ, rms for separated residues. Catein Catherine
- [AMBER] correlation motion at production simulation period still changing. Is it normal? Catein Catherine
- Re: [AMBER] PTRAJ, rms for separated residues. Germain Vallverdu
- [AMBER] Atom Type List Javier Klett
- [AMBER] About the Amber tutorial Aurum Bai
- [AMBER] About the "FATAL: Atom err!" Aurum Bai
- [AMBER] About the "FATAL: Atom err"! Aurum Bai
- [AMBER] Error on equilibriation of Amber10 Masakazu SEKIJIMA
- Re: [AMBER] Atom Type List case
- Re: [AMBER] About the "FATAL: Atom err"! case
- [AMBER] max atoms for antechamber Alan
- Re: [AMBER] max atoms for antechamber case
- Re: [AMBER] max atoms for antechamber Alan
- [AMBER] making leap to recognize 5' phosphate Bala subramanian
- Re: [Barracuda SPAM] Re: [AMBER] Atom Type List Javier Klett
- Re: [Barracuda SPAM] Re: [AMBER] Atom Type List Bill Ross
- [AMBER] Re: Regd: Fe4S4 case
- RE: [Subject Filtered] Re: [AMBER] Amber10 Parallel Installation 8% Hopkins, Robert
- [AMBER] bad atom type: MN Edward M
- [AMBER] bad atom type: MN Edward M
- RE: [AMBER] reclaiming space from amber10 installation Ross Walker
- RE: [AMBER] Hard limit in Amber10? Yang, Ping
- [AMBER] AMBER question: bad atom type: MN Edward M
- [AMBER] REMD Shaikh Abdul R S Ramaju
Tuesday, 23 June 2009
- Re: [AMBER] making leap to recognize 5' phosphate FyD
- [AMBER] guessing the charge of a small molecule Alan
- Re: [AMBER] making leap to recognize 5' phosphate Bala subramanian
- Re: [AMBER] making leap to recognize 5' phosphate FyD
- Re: [AMBER] REMD Carlos Simmerling
- [AMBER] Compiling amber 9 with openMPI Myunggi Yi
- Re: [AMBER] Compiling amber 9 with openMPI case
- [AMBER] net charge Vishal Maingi
- Re: [AMBER] net charge case
- [AMBER] SANDER BOMB in subroutine nonbond_list Siddharth Rastogi
- Re: [AMBER] SANDER BOMB in subroutine nonbond_list Bill Ross
- Re: [AMBER] Compiling amber 9 with openMPI Myunggi Yi
- [AMBER] re: net charge Vishal Maingi
- Re: [AMBER] re: net charge case
- Re: [AMBER] re: net charge Junmei Wang
- [AMBER] "loadoff tRNA.lib" in Leap Ju Zhang
- [AMBER] 2-step vs 3-step TI, and softcores question Jodi Hadden
- Re: [AMBER] 2-step vs 3-step TI, and softcores question steinbrt.rci.rutgers.edu
- [AMBER] How to build amide bond etween two protein chains journal.update
- [AMBER] error in tleap of AMBER 10 kureeckal ramesh
- Re: [AMBER] making leap to recognize 5' phosphate FyD
- [AMBER] Problems using nmode in NAB E.M.
- Re: [AMBER] How to build amide bond etween two protein chains FyD
Wednesday, 24 June 2009
- Re: [AMBER] Problems using nmode in NAB Andreas Svrcek-Seiler
- Re: [AMBER] Problems using nmode in NAB E.M.
- [AMBER] calculating the hydrogen bonding energy between the two molecule bharat lakhani
- [AMBER] Trying to patch amber 9 Jack Shultz
- Re: [AMBER] Trying to patch amber 9 case
- Re: [AMBER] Trying to patch amber 9 Jack Shultz
- Re: [AMBER] Trying to patch amber 9 Jack Shultz
- RE: [AMBER] Hard limit in Amber10? Ross Walker
- [AMBER] Half charge reported during NN ? Marek Maly
- Re: [AMBER] Half charge reported during NN ? case
- Re: [AMBER] Half charge reported during NN ? Marek Maly
- [AMBER] problem with parametrization janzso.brc.hu
- RE: [AMBER] problem with parametrization Brothers, Michael Charles
- [AMBER] Amber tools 1.2 , Bug report (PTRAJ: dumpq with strip) Myunggi Yi
- [AMBER] NAB memory increase E.M.
- [AMBER] setting atomic radii for GB version 7 Workalemhu Berhanu
- Re: [AMBER] Problems using nmode in NAB E.M.
- Re: [AMBER] problem with parametrization FyD
Thursday, 25 June 2009
- Re: [AMBER] atomtypes in gaff FyD
- [AMBER] Re: question about ff FyD
- [AMBER] ADD SALT Rilei Yu
- AW: [AMBER] atomtypes in gaff Aust, Susanne
- Re: [AMBER] problem with parametrization janzso.brc.hu
- Re: [AMBER] ADD SALT Simon Becker
- Re: [AMBER] problem with parametrization FyD
- Re: AW: [AMBER] atomtypes in gaff FyD
- [AMBER] Re: Error on equilibriation of Amber10 Masakazu SEKIJIMA
- [AMBER] IGB=7 vs IGB=5 guardiani.fi.infn.it
- AW: AW: [AMBER] atomtypes in gaff Aust, Susanne
- Re: [AMBER] NAB memory increase case
- Re: AW: AW: [AMBER] atomtypes in gaff FyD
- Re: [AMBER] problem with parametrization janzso.brc.hu
- [AMBER] PCA for CA of specific resiudes Patrick Gedeon
- Re: [AMBER] atomtypes in gaff FyD
- AW: AW: AW: [AMBER] atomtypes in gaff Aust, Susanne
- Re: [AMBER] problem with parametrization FyD
- Re: [AMBER] error in tleap of AMBER 10 case
- Re: [AMBER] problem with parametrization janzso.brc.hu
- AW: [AMBER] atomtypes in gaff Aust, Susanne
- Re: [AMBER] Re: Error on equilibriation of Amber10 case
- [AMBER] Error when installing amber11 on OpenSuse steinbrt.rci.rutgers.edu
- Re: [AMBER] setting atomic radii for GB version 7 case
- Re: [AMBER] PCA for CA of specific resiudes case
- [AMBER] ADD SALT additional question Simon Becker
- Re: [AMBER] Problems using nmode in NAB Andreas Svrcek-Seiler
- Re: [AMBER] problem with parametrization FyD
- Re: [AMBER] ADD SALT additional question Vlad Cojocaru
- Re: [AMBER] ADD SALT additional question Vlad Cojocaru
- [AMBER] ptraj clustering with sieve- unexpected Bus Error Rachel Rice
- Re: [AMBER] NAB memory increase Bill Ross
- Re: AW: [AMBER] atomtypes in gaff Bill Ross
- Re: [AMBER] Re: Error on equilibriation of Amber10 Masakazu SEKIJIMA
- Re: [AMBER] ptraj clustering with sieve- unexpected Bus Error David Watson
- [AMBER] Compiling and running NAB programs in parallel using MPI Kaushik Raha
- [AMBER] Thanks Simon and Vlad! Rilei Yu
- Re: [AMBER] ptraj clustering with sieve- unexpected Bus Error Rachel Rice
- Re: [AMBER] ptraj clustering with sieve- unexpected Bus Error David Watson
- Re: [AMBER] ptraj clustering with sieve- unexpected Bus Error Rachel Rice
- Re: [AMBER] ptraj clustering with sieve- unexpected Bus Error David Watson
- Re: [AMBER] ptraj clustering with sieve- unexpected Bus Error Rachel Rice
- Re: AW: [AMBER] atomtypes in gaff FyD
Friday, 26 June 2009
- [AMBER] error in tleap of AMBER 10 kureeckal ramesh
- [AMBER] Box Center Jagan Mohan
- [AMBER] installation of RESP programm subarna thakur
- [AMBER] Problem with radial distribution function aneesh cna
- Re: [AMBER] installation of RESP programm FyD
- [AMBER] query about the charge fitting procedure about C- and N-terminal residues Ye MEI
- Re: [AMBER] query about the charge fitting procedure about C- and N-terminal residues FyD
- [AMBER] a method or program to try to guess the net charge of a small molecule Alan
- Re: [AMBER] ptraj clustering with sieve- unexpected Bus Error David Watson
- Re: [AMBER] error in tleap of AMBER 10 case
- Re: [AMBER] Re: Error on equilibriation of Amber10 case
- Re: [AMBER] Compiling and running NAB programs in parallel using MPI case
- Re: [AMBER] Compiling and running NAB programs in parallel using MPI Kaushik Raha
- [AMBER] force field choice ahmed said
- [AMBER] NAB memory E.M.
- Re: [AMBER] NAB memory case
Saturday, 27 June 2009
- Re: [AMBER] how to know that adequate equilibration from rmsd curve of equilibration Cihan Aydin
- Re: [AMBER] how to know that adequate equilibration from rmsd curve of equilibration Naser Alijabbari
Sunday, 28 June 2009
- [AMBER] explicit solvent NMR refinement Sally Pias
- Re: [AMBER] explicit solvent NMR refinement Carlos Simmerling
- Re: [AMBER] explicit solvent NMR refinement case
- [AMBER] Velocity rescaling and ig... Cihan Aydin
- Re: [AMBER] Velocity rescaling and ig... Carlos Simmerling
- [AMBER] how to creat an mixture sovlent of hexane and water TaoPaul
- Re: [AMBER] Velocity rescaling and ig... Cihan Aydin
- RE: [AMBER] Velocity rescaling and ig... Ross Walker
- Re: [AMBER] how to know that adequate equilibration from rmsd curve of equilibration Cihan Aydin
- RE: [AMBER] Velocity rescaling and ig... Cihan Aydin
- [AMBER] Analysis of the solt-bridge Rilei Yu
- [AMBER] Simulations including RNA-protein complexes... Cihan Aydin
Monday, 29 June 2009
- [AMBER] RESP Syed Tarique Moin
- Re: [AMBER] problem with parametrization janzso.brc.hu
- Re: [AMBER] RESP case
- Re: [AMBER] Compiling and running NAB programs in parallel using MPI case
- Re: [AMBER] Analysis of the solt-bridge Alessandro Nascimento
- [AMBER] Steps for NMR structure minimization Prem Prakash Pathak
- [AMBER] steps for NMR structure minimization of protein Prem Prakash Pathak
- [AMBER] steps for NMR structure minimization of protein Prem Prakash Pathak
- [AMBER] problems with ptraj option IMAGE Antonija Tomić
- Re: [AMBER] problems with ptraj option IMAGE Carlos Simmerling
- Re: [AMBER] problems with ptraj option IMAGE Antonija Tomić
- [AMBER] Regd: parameter Fe4S4 KIRTANA S
- [AMBER] Nonstandard molecules simulated with parm99EP ? Marek Maly
- Re: [AMBER] Nonstandard molecules simulated with parm99EP ? FyD
- Re: [AMBER] Regd: parameter Fe4S4 FyD
- Re: [AMBER] Nonstandard molecules simulated with parm99EP ? Marek Maly
- Re: [AMBER] Analysis of the solt-bridge Rilei Yu
- [AMBER] Fe-S topology subarna thakur
Tuesday, 30 June 2009
- Re: [AMBER] Fe-S topology Markus Kaukonen
- Re: [AMBER] Nonstandard molecules simulated with parm99EP ? FyD
- [AMBER] Saccharides chains termini Sergey Samsonov
- Re: [AMBER] Saccharides chains termini Lachele Foley (Lists)
- Re: [AMBER] Compiling and running NAB programs in parallel using MPI Kaushik Raha
- Re: [AMBER] Saccharides chains termini Karl Kirschner
- Re: [AMBER] ptraj clustering with sieve- unexpected Bus Error Rachel Rice
- Re: [AMBER] Saccharides chains termini FyD
- Re: [AMBER] Compiling and running NAB programs in parallel using MPI case
- Re: [AMBER] Nonstandard molecules simulated with parm99EP ? case
- Re: [AMBER] Fe-S topology case
- [AMBER] Partial charges of heme Justine Shaw Condo
- [AMBER] Fe and Mn simulations Alessandro Nascimento

Last message date: Mon Jul 06 2009 - 12:23:12 PDT
Archived on: Wed Apr 24 2024 - 05:53:51 PDT

Amber Archive Jun 2009 by date