Amber Archive May 2015: by date

Friday, 1 May 2015
- [AMBER] Implicit water for MD studies Shreeramesh
- Re: [AMBER] Implicit water for MD studies Jason Swails
- [AMBER] CPPTRAJ V12.1 principal axis different to V13.22 and V14.25 CHAMI F.
- [AMBER] Solvation of a long protein Steven Ramsey
- Re: [AMBER] Solvation of a long protein amin.imtech.res.in
- Re: [AMBER] Solvation of a long protein Jason Swails
- Re: [AMBER] CPPTRAJ V12.1 principal axis different to V13.22 and V14.25 Daniel Roe
- Re: [AMBER] Solvation of a long protein Daniel Roe
- Re: [AMBER] Implicit water for MD studies Carlos Simmerling
- Re: [AMBER] CPPTRAJ V12.1 principal axis different to V13.22 and V14.25 CHAMI F.
- Re: [AMBER] Solvation of a long protein Steven Ramsey
Saturday, 2 May 2015
- [AMBER] cpptraj: Per residue rmsd George Tzotzos
- Re: [AMBER] cpptraj: Per residue rmsd Daniel Roe
Sunday, 3 May 2015
- Re: [AMBER] cpptraj: Per residue rmsd George Tzotzos
- Re: [AMBER] error in amber installation Atila Petrosian
- Re: [AMBER] error in amber installation David A Case
- Re: [AMBER] error in amber installation Atila Petrosian
- Re: [AMBER] error in amber installation David A Case
- Re: [AMBER] error in amber installation Jason Swails
Monday, 4 May 2015
- Re: [AMBER] Implicit water for MD studies Shreeramesh
- Re: [AMBER] Implicit water for MD studies Debayan Chakraborty
- [AMBER] Problem Regarding PMF Graph Shubhadip Das
- [AMBER] Fw: Problem Regarding PMF Graph Shubhadip Das
- [AMBER] Problem regarding PMF curve Shubhadip Das
- Re: [AMBER] Implicit water for MD studies Jason Swails
- [AMBER] Announcement: Release of AmberTools15 David A Case
- Re: [AMBER] Fw: Problem Regarding PMF Graph Adrian Roitberg
- [AMBER] amber tools 15 upgrade problem Michael Shokhen
- Re: [AMBER] amber tools 15 upgrade problem Daniel Roe
- Re: [AMBER] amber tools 15 upgrade problem Kenneth Huang
- Re: [AMBER] amber tools 15 upgrade problem Michael Shokhen
- Re: [AMBER] amber tools 15 upgrade problem Jason Swails
- Re: [AMBER] amber tools 15 upgrade problem David A Case
- Re: [AMBER] amber tools 15 upgrade problem Kenneth Huang
- [AMBER] representing structure from equilibrium newamber list
- Re: [AMBER] amber tools 15 upgrade problem David A Case
- Re: [AMBER] error in amber installation Atila Petrosian
- Re: [AMBER] error in amber installation Jason Swails
- [AMBER] MM_PBSA analysis Ramin Ekhteiari
- Re: [AMBER] MM_PBSA analysis Jason Swails
- Re: [AMBER] error in amber installation Atila Petrosian
- [AMBER] Difference between EXTDIEL and EPSOUT? Chinh Su Tran To
Tuesday, 5 May 2015
- [AMBER] Is it necessary to cap the N and C terminal using ACE and NHE in tleap? Wang Moye
- [AMBER] forcefield for DNA 王珍
- Re: [AMBER] Is it necessary to cap the N and C terminal using ACE and NHE in tleap? Carlos Simmerling
- Re: [AMBER] error in amber installation David A Case
- Re: [AMBER] forcefield for DNA David A Case
- Re: [AMBER] Difference between EXTDIEL and EPSOUT? Jason Swails
- Re: [AMBER] forcefield for DNA 王珍
- Re: [AMBER] forcefield for DNA Thomas C. Bishop
- Re: [AMBER] forcefield for DNA Christina Bergonzo
- [AMBER] IRED Sylvester Tumusiime
- Re: [AMBER] IRED Christina Bergonzo
- Re: [AMBER] IRED Sylvester Tumusiime
- Re: [AMBER] IRED Christina Bergonzo
- Re: [AMBER] IRED Sylvester Tumusiime
- [AMBER] Computational Chemical Biology Conference - Abstract Deadline May 15th Ross Walker
- [AMBER] GPCR-MM_PBSA Ramin Ekhteiari
- [AMBER] GPCR-MM_PBSA Ramin Ekhteiari
- [AMBER] GPCR-MM_PBSA Ramin Ekhteiari
- Re: [AMBER] GPCR-MM_PBSA Holger Gohlke
- Re: [AMBER] Is it necessary to cap the N and C terminal using ACE and NHE in tleap? Wang Moye
Wednesday, 6 May 2015
- [AMBER] Atome type fatal error Pierre Bertin
- Re: [AMBER] Atome type fatal error Hannes Loeffler
- [AMBER] Query on how to simulate bulk no.of molecules in AMBER srilaxmi reddy
- Re: [AMBER] Query on how to simulate bulk no.of molecules in AMBER Ashutosh Shandilya
- [AMBER] Error when compile ambertools15 amber amber
- [AMBER] CUDA compiling of Amber tools 14 anu chandra
- Re: [AMBER] CUDA compiling of Amber tools 14 Jason Swails
- Re: [AMBER] Error when compile ambertools15 Jason Swails
- Re: [AMBER] Atome type fatal error David A Case
- Re: [AMBER] Query on how to simulate bulk no.of molecules in AMBER Jason Swails
- Re: [AMBER] Nmode analysis calculation problem for Implicit simulation. Bajarang Kumbhar
- [AMBER] MMPBSA.py Ramin Ekhteiari
- Re: [AMBER] MMPBSA.py David A Case
- Re: [AMBER] Nmode analysis calculation problem for Implicit simulation. David A Case
- [AMBER] Trouble understanding DBSCAN clustering algorithm Juan Eiros Zamora
- [AMBER] Error with running ParmEd Yinglong Miao
- Re: [AMBER] Trouble understanding DBSCAN clustering algorithm Christina Bergonzo
- Re: [AMBER] Trouble understanding DBSCAN clustering algorithm Daniel Roe
- Re: [AMBER] MMPBSA.py Ramin Ekhteiari
- Re: [AMBER] MMPBSA.py David A Case
- Re: [AMBER] MMPBSA.py Ramin Ekhteiari
- Re: [AMBER] MMPBSA.py Jason Swails
- Re: [AMBER] Error with running ParmEd Jason Swails
- [AMBER] Replica-exchange molecular dynamics 新生大侠
- Re: [AMBER] MMPBSA.py Ramin Ekhteiari
Thursday, 7 May 2015
- [AMBER] leap: adding a residue to a unit Hannes Loeffler
- Re: [AMBER] Trouble understanding DBSCAN clustering algorithm Juan Eiros Zamora
- Re: [AMBER] Replica-exchange molecular dynamics Carlos Simmerling
- [AMBER] CpHMD for Ser residue? Michael Shokhen
- Re: [AMBER] Implicit water for MD studies Shreeramesh
- Re: [AMBER] amber tools 15 upgrade problem Michael Shokhen
- Re: [AMBER] CpHMD for Ser residue? Jason Swails
- Re: [AMBER] CpHMD for Ser residue? Carlos Simmerling
- [AMBER] bad atom type: Ng (*.prmtop files from tleap) Carlos Modenutti
- [AMBER] Error when compile ambertools15 amber amber
- Re: [AMBER] MMPBSA.py Jason Swails
- Re: [AMBER] MMPBSA.py Jason Swails
- [AMBER] query parameter files for mercuric ions Ya Gao
- Re: [AMBER] Error when compile ambertools15 Jason Swails
- Re: [AMBER] bad atom type: Ng (*.prmtop files from tleap) Jason Swails
- Re: [AMBER] query parameter files for mercuric ions Pengfei Li
- [AMBER] box's information Fatemeh Sadat Alavi
- Re: [AMBER] box's information Jason Swails
- [AMBER] problem with prepgen in an organic molecule parameterization Rebeca García Fandiño
- Re: [AMBER] problem with prepgen in an organic molecule parameterization Daniel Roe
- Re: [AMBER] problem with prepgen in an organic molecule parameterization Rebeca García Fandiño
- Re: [AMBER] Trouble understanding DBSCAN clustering algorithm Daniel Roe
- [AMBER] Assistance required installing amber in cuda Bala Subramani
- Re: [AMBER] bad atom type: Ng (*.prmtop files from tleap) Daniel Roe
- Re: [AMBER] problem with prepgen in an organic molecule parameterization Daniel Roe
- Re: [AMBER] Assistance required installing amber in cuda Daniel Roe
- Re: [AMBER] bad atom type: Ng (*.prmtop files from tleap) Carlos Modenutti
- Re: [AMBER] Error with running ParmEd Yinglong Miao
- Re: [AMBER] MMPBSA.py Ramin Ekhteiari
- Re: [AMBER] problem with prepgen in an organic molecule parameterization Rebeca García Fandiño
- Re: [AMBER] Assistance required installing amber in cuda Bala Subramani
- Re: [AMBER] Assistance required installing amber in cuda Bala Subramani
- Re: [AMBER] problem with prepgen in an organic molecule parameterization Daniel Roe
- Re: [AMBER] Assistance required installing amber in cuda Jason Swails
- Re: [AMBER] Error with running ParmEd Jason Swails
- Re: [AMBER] Atome type fatal error Pierre Bertin
- Re: [AMBER] MMPBSA problem with calcium Francesco Gentile
- Re: [AMBER] Error when compile ambertools15 Yu Chen
- Re: [AMBER] Error when compile ambertools15 Jason Swails
- Re: [AMBER] Error when compile ambertools15 Yu Chen
Friday, 8 May 2015
- Re: [AMBER] box's information Fatemeh Sadat Alavi
- [AMBER] Error when compile ambertools15 amber amber
- Re: [AMBER] problem with prepgen in an organic molecule parameterization Rebeca García Fandiño
- [AMBER] Faulty_atom_connection error nibedita jana
- [AMBER] MCPB error Takeshi Baba
- Re: [AMBER] Error when compile ambertools15 Jason Swails
- Re: [AMBER] box's information Jason Swails
- Re: [AMBER] Faulty_atom_connection error David A Case
- Re: [AMBER] box's information David A Case
- Re: [AMBER] leap: adding a residue to a unit David A Case
- Re: [AMBER] Trouble understanding DBSCAN clustering algorithm Juan Eiros Zamora
- Re: [AMBER] Trouble understanding DBSCAN clustering algorithm Daniel Roe
- Re: [AMBER] MCPB error Pengfei Li
- [AMBER] cpptraj checkoverlap Aronica, Pietro
- Re: [AMBER] cpptraj checkoverlap Jason Swails
- Re: [AMBER] cpptraj checkoverlap Aronica, Pietro
- Re: [AMBER] cpptraj checkoverlap Daniel Roe
- Re: [AMBER] cpptraj checkoverlap Daniel Roe
- [AMBER] MMPBSA.py.MPI George Tzotzos
- Re: [AMBER] MM_PBSA analysis Hai Nguyen
- Re: [AMBER] MCPB error Takeshi Baba
Saturday, 9 May 2015
- Re: [AMBER] MM_PBSA analysis Ramin Ekhteiari
- Re: [AMBER] MM_PBSA analysis Vlad Cojocaru
- Re: [AMBER] MM_PBSA analysis Ramin Ekhteiari
- Re: [AMBER] MM_PBSA analysis Vlad Cojocaru
- Re: [AMBER] MMPBSA.py.MPI Jason Swails
- [AMBER] The output file about SMD wjli
- [AMBER] Problem with Configuring NetCDF Alaa Mohye El-din Soliman
- Re: [AMBER] Problem with Configuring NetCDF Jason Swails
- [AMBER] question regarding SMD simulation Asmita Gupta
- Re: [AMBER] The output file about SMD Jason Swails
- [AMBER] Selection of chain muhammad tahir ayub
- Re: [AMBER] Problem with Configuring NetCDF Alaa Mohye El-din Soliman
- [AMBER] QM/MM Protein-Ligand interaction w/cofactor William Martin
- Re: [AMBER] Problem with Configuring NetCDF Jason Swails
- Re: [AMBER] QM/MM Protein-Ligand interaction w/cofactor Gustavo Seabra
- Re: [AMBER] Selection of chain David A Case
- Re: [AMBER] QM/MM Protein-Ligand interaction w/cofactor David A Case
- Re: [AMBER] QM/MM Protein-Ligand interaction w/cofactor William Martin
Sunday, 10 May 2015
- [AMBER] Fwd: Selection of chain muhammad tahir ayub
- Re: [AMBER] Fwd: Selection of chain Kenneth Huang
- [AMBER] parameters for type: Cl- Michael Shokhen
- Re: [AMBER] parameters for type: Cl- Kenneth Huang
- Re: [AMBER] parameters for type: Cl- Michael Shokhen
- Re: [AMBER] parameters for type: Cl- Marc van der Kamp
- Re: [AMBER] parameters for type: Cl- David A Case
- Re: [AMBER] Problem with Configuring NetCDF Alaa Mohye El-din Soliman
- [AMBER] Algorithms for integrating the equations of motion gepaula.web.de
- Re: [AMBER] Algorithms for integrating the equations of motion Hai Nguyen
- Re: [AMBER] Problem with Configuring NetCDF Jason Swails
- [AMBER] qmcut in Amber14 Manual Robert Molt
- [AMBER] restart an SMD run Asmita Gupta
Monday, 11 May 2015
- Re: [AMBER] qmcut in Amber14 Manual Marc van der Kamp
- [AMBER] Error while running tleap for protein-RNA complex Shreeramesh
- [AMBER] principal component analysis abdennour braka
- Re: [AMBER] Error while running tleap for protein-RNA complex Hector A. Baldoni
- Re: [AMBER] Error while running tleap for protein-RNA complex David A Case
- Re: [AMBER] qmcut in Amber14 Manual Jason Swails
- Re: [AMBER] restart an SMD run Jason Swails
- [AMBER] AMD with restrained molecule. Binwu Zhao
- [AMBER] mmpbsa.py error George Tzotzos
- Re: [AMBER] mmpbsa.py error Jason Swails
- Re: [AMBER] mmpbsa.py error George Tzotzos
- [AMBER] parallel installation of ambertools14 on centOS-rocks system Andrew Bostick
- Re: [AMBER] parallel installation of ambertools14 on centOS-rocks system Jason Swails
- Re: [AMBER] principal component analysis Daniel Roe
- Re: [AMBER] representing structure from equilibrium Daniel Roe
- Re: [AMBER] representing structure from equilibrium newamber list
Tuesday, 12 May 2015
- [AMBER] experimental coulomb and van der Waals cutoffs Ahmet yıldırım
- Re: [AMBER] Error while running tleap for protein-RNA complex Shreeramesh
- Re: [AMBER] experimental coulomb and van der Waals cutoffs Carlos Simmerling
- [AMBER] How to fix missing residues Shreeramesh
- Re: [AMBER] experimental coulomb and van der Waals cutoffs Ahmet yıldırım
- Re: [AMBER] How to fix missing residues Sajeewa Pemasinghe
- Re: [AMBER] restart an SMD run Asmita Gupta
- Re: [AMBER] restart an SMD run Jason Swails
- Re: [AMBER] experimental coulomb and van der Waals cutoffs Jason Swails
- Re: [AMBER] restart an SMD run Asmita Gupta
- Re: [AMBER] Error while running tleap for protein-RNA complex Jason Swails
- Re: [AMBER] restart an SMD run Jason Swails
- [AMBER] mmpbsa.py: new error message George Tzotzos
- [AMBER] mmpbsa.py: new error message Kenneth Huang
- [AMBER] pmemd performance on GTX Titan Z Kenneth Huang
- Re: [AMBER] mmpbsa.py: new error message Jason Swails
- Re: [AMBER] mmpbsa.py: new error message George Tzotzos
- Re: [AMBER] mmpbsa.py: new error message Jason Swails
- Re: [AMBER] pmemd performance on GTX Titan Z Ross Walker
Wednesday, 13 May 2015
- [AMBER] Atoms overlapped in vacuum minimization anu chandra
- Re: [AMBER] Atoms overlapped in vacuum minimization Carlos Simmerling
- Re: [AMBER] Atoms overlapped in vacuum minimization David A Case
- Re: [AMBER] Atoms overlapped in vacuum minimization anu chandra
- [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" James Starlight
- Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" Vlad Cojocaru
- Re: [AMBER] Atoms overlapped in vacuum minimization Carlos Simmerling
- [AMBER] Principal moments of inertia Sylvester Tumusiime
- [AMBER] site down? Gerald Monard
- Re: [AMBER] site down? Akash Deep Biswas
- Re: [AMBER] site down? Marc van der Kamp
- Re: [AMBER] site down? Gerald Monard
- Re: [AMBER] site down? Jonathan Gough
- Re: [AMBER] site down? Ross Walker
- Re: [AMBER] site down? Ross Walker
- Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" James Starlight
- Re: [AMBER] site down? Gerald Monard
- [AMBER] adp amber parameters Carlos Romero
- Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" Vlad Cojocaru
- [AMBER] error using the lipidorder command Sylvester Tumusiime
- [AMBER] Amber website down Crystal VanderZanden
- Re: [AMBER] Amber website down James Maier
- Re: [AMBER] site down? Jason Swails
- Re: [AMBER] adp amber parameters David A Case
- Re: [AMBER] adp amber parameters Carlos Romero
- [AMBER] DOPC lipid bilayer in Amber using lipid14 force field. Him Shweta
- [AMBER] Question about lipid simulation Victor Ma
- Re: [AMBER] Question about lipid simulation Ross Walker
- Re: [AMBER] DOPC lipid bilayer in Amber using lipid14 force field. Ross Walker
- [AMBER] ante-mmpbsa.py: troubleshooting George Tzotzos
- Re: [AMBER] ante-mmpbsa.py: troubleshooting Jason Swails
- Re: [AMBER] ante-mmpbsa.py: troubleshooting George Tzotzos
- Re: [AMBER] ante-mmpbsa.py: troubleshooting Jason Swails
- Re: [AMBER] ante-mmpbsa.py: troubleshooting George Tzotzos
- Re: [AMBER] cpptraj checkoverlap Daniel Roe
- [AMBER] Error selecting compatible GPU all CUDA-capable devices are busy or unavailable Jagga Soorma
- [AMBER] Praise Dr. Robert Molt Jr.
- [AMBER] pmemd performance on GTX Titan Z Kenneth Huang
- Re: [AMBER] site down? Wang Moye
- Re: [AMBER] Amber website down Wang Moye
Thursday, 14 May 2015
- Re: [AMBER] site down? Gerald Monard
- Re: [AMBER] site down? David A Case
- Re: [AMBER] Principal moments of inertia Daniel Roe
- Re: [AMBER] error using the lipidorder command Daniel Roe
- Re: [AMBER] Error selecting compatible GPU all CUDA-capable devices are busy or unavailable Jason Swails
- [AMBER] minimization error Carlos Romero
- Re: [AMBER] minimization error Jason Swails
- Re: [AMBER] minimization error Carlos Romero
- [AMBER] Warning when trying to get RMS Mohammad Salem
- Re: [AMBER] Warning when trying to get RMS Daniel Roe
- [AMBER] Announcement: GLYCAM/GLYCAM-Web mailing list Lachele Foley
- [AMBER] How to run GBSA in MD and binding energy calculation (MMPBSA.py)? Huang
- Re: [AMBER] Fw: Problem Regarding PMF Graph Shubhadip Das
Friday, 15 May 2015
- [AMBER] Arsenic force field parametrization Sushi Shilpa
- [AMBER] ESURF in MMPBSA.py results Huang
- Re: [AMBER] How to run GBSA in MD and binding energy calculation (MMPBSA.py)? Jason Swails
- [AMBER] the energy between two ligand molecules chemjxn
- Re: [AMBER] ESURF in MMPBSA.py results Jason Swails
- Re: [AMBER] the energy between two ligand molecules Jason Swails
- Re: [AMBER] Fw: Problem Regarding PMF Graph Jason Swails
- Re: [AMBER] How to run GBSA in MD and binding energy calculation (MMPBSA.py)? Carlos Simmerling
- Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" James Starlight
- [AMBER] Biligand, trimetal subtrate simulation Julio Dominguez
- Re: [AMBER] MMPBSA.py.MPI George Tzotzos
- [AMBER] disable minimization in nmode MMPBSA.py Carlos Modenutti
- Re: [AMBER] disable minimization in nmode MMPBSA.py Jason Swails
- Re: [AMBER] MMPBSA.py.MPI Jason Swails
Saturday, 16 May 2015
- [AMBER] Help needed on MMPBSA for a system with different protonation states in free & bound forms, using multiple trajectory protocol Shailesh Pandey
- Re: [AMBER] MMPBSA.py.MPI George Tzotzos
- Re: [AMBER] MMPBSA.py.MPI Jason Swails
- Re: [AMBER] Help needed on MMPBSA for a system with different protonation states in free & bound forms, using multiple trajectory protocol Jason Swails
- Re: [AMBER] MMPBSA.py.MPI George Tzotzos
- Re: [AMBER] Arsenic force field parametrization Andrew Schaub
Sunday, 17 May 2015
- [AMBER] Regarding - "Help needed on MMPBSA for a system with different protonation states in free & bound forms" Shailesh Pandey
- [AMBER] Polymorphism study using Amber jacob wick
Monday, 18 May 2015
- Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" James Starlight
- [AMBER] Changing two conditions simultaneously in pmemd Juan Eiros Zamora
- Re: [AMBER] Polymorphism study using Amber David A Case
- Re: [AMBER] Changing two conditions simultaneously in pmemd Hannes Loeffler
- Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" Vlad Cojocaru
- [AMBER] WEBSITE not opening Elvis Martis
- Re: [AMBER] WEBSITE not opening Jason Swails
- Re: [AMBER] Regarding - "Help needed on MMPBSA for a system with different protonation states in free & bound forms" Jason Swails
- Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" James Starlight
- Re: [AMBER] Changing two conditions simultaneously in pmemd Juan Eiros Zamora
- Re: [AMBER] Changing two conditions simultaneously in pmemd Hannes Loeffler
- Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" Vlad Cojocaru
- Re: [AMBER] Changing two conditions simultaneously in pmemd Vlad Cojocaru
- Re: [AMBER] Changing two conditions simultaneously in pmemd Vlad Cojocaru
- Re: [AMBER] Changing two conditions simultaneously in pmemd Juan Eiros Zamora
- Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" James Starlight
- Re: [AMBER] Changing two conditions simultaneously in pmemd Hannes Loeffler
- Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" James Starlight
- Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" Vlad Cojocaru
- Re: [AMBER] Changing two conditions simultaneously in pmemd Jason Swails
- Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" Vlad Cojocaru
- Re: [AMBER] Changing two conditions simultaneously in pmemd Vlad Cojocaru
- Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" Vlad Cojocaru
- Re: [AMBER] Changing two conditions simultaneously in pmemd Christina Bergonzo
- Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" James Starlight
- Re: [AMBER] Changing two conditions simultaneously in pmemd Hannes Loeffler
- Re: [AMBER] Regarding - "Help needed on MMPBSA for a system with different protonation states in free & bound forms" Shailesh Pandey
- Re: [AMBER] Changing two conditions simultaneously in pmemd Ross Walker
- Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" Vlad Cojocaru
- Re: [AMBER] Changing two conditions simultaneously in pmemd Vlad Cojocaru
- Re: [AMBER] Arsenic force field parametrization Pengfei Li
- Re: [AMBER] WEBSITE not opening Elvis Martis
- Re: [AMBER] WEBSITE not opening Ross Walker
- Re: [AMBER] WEBSITE not opening Ye Mei
Tuesday, 19 May 2015
- [AMBER] Problem with amb2gmx in AmberTools 15 Soumendranath Bhakat
- Re: [AMBER] Problem with amb2gmx in AmberTools 15 David A Case
- Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" James Starlight
- Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" James Starlight
- Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" Vlad Cojocaru
- Re: [AMBER] DNS manipulations David A Case
Thursday, 14 May 2015
- [AMBER] Sander QMMM Bomb Problem Gulsevin,Alican
Tuesday, 19 May 2015
- [AMBER] Computational Chemical Biology Conference - TALK DEADLINE EXTENDED Ross Walker
- Re: [AMBER] DNS manipulations Ross Walker
- Re: [AMBER] Sander QMMM Bomb Problem Gustavo Seabra
- [AMBER] MCPB.py issues David Poole
- [AMBER] Computational Chemical Biology Conference - Abstract Deadline Extended to June 1st Ross Walker
- Re: [AMBER] DNS manipulations Bill Ross
- [AMBER] problems with "explicit solvent" Investigador Química
- Re: [AMBER] problems with "explicit solvent" David A Case
- Re: [AMBER] WEBSITE not opening Elvis Martis
- [AMBER] MC-simulation-MM-PBSA Ramin Ekhteiari
Wednesday, 20 May 2015
- Re: [AMBER] Problem with amb2gmx in AmberTools 15 Soumendranath Bhakat
- Re: [AMBER] Problem with amb2gmx in AmberTools 15 Hannes Loeffler
- Re: [AMBER] Problem with amb2gmx in AmberTools 15 Soumendranath Bhakat
- Re: [AMBER] Problem with amb2gmx in AmberTools 15 Soumendranath Bhakat
- Re: [AMBER] Problem with amb2gmx in AmberTools 15 Hannes Loeffler
- Re: [AMBER] Problem with amb2gmx in AmberTools 15 David A Case
- Re: [AMBER] MCPB.py issues David A Case
- [AMBER] MMGBSA: interpretation of results George Tzotzos
- Re: [AMBER] Problem with amb2gmx in AmberTools 15 Soumendranath Bhakat
- [AMBER] Amber12 + GTX 980 Robinson, Roger
- [AMBER] Amber 12 + GTX 980 Robinson, Roger
- Re: [AMBER] MCPB.py issues Pengfei Li
- [AMBER] AMBERHOME environment variable setting problem Gustavo Avelar Molina
- Re: [AMBER] AMBERHOME environment variable setting problem Jason Swails
- Re: [AMBER] Amber 12 + GTX 980 Ross Walker
- Re: [AMBER] Problem with amb2gmx in AmberTools 15 Soumendranath Bhakat
- Re: [AMBER] AMBERHOME environment variable setting problem MOHD HOMAIDUR RAHMAN
- Re: [AMBER] MMGBSA: interpretation of results George Tzotzos
- Re: [AMBER] MMGBSA: interpretation of results Kenneth Huang
- [AMBER] Bad Contact from lack of QM/MM Heating? Dr. Robert Molt Jr.
- [AMBER] MC-MM-PBSA Ramin Ekhteiari
- Re: [AMBER] Amber 12 + GTX 980 Robinson, Roger
Thursday, 21 May 2015
- Re: [AMBER] MC-MM-PBSA Jason Swails
- Re: [AMBER] Amber 12 + GTX 980 Scott Le Grand
Friday, 22 May 2015
- [AMBER] Question about Extra Point zhouhaibin2008.ok
- [AMBER] Regarding AMD simulation Aditya Sarkar
- Re: [AMBER] Question about Extra Point David A Case
- [AMBER] Does GLYCAM only can deal with Oligosaccharides or Polysaccharides BUT NOT Monosaccharide？？？ Chris
- Re: [AMBER] Regarding AMD simulation Daniel Roe
- Re: [AMBER] Does GLYCAM only can deal with Oligosaccharides or Polysaccharides BUT NOT Monosaccharide？？？ Lachele Foley
- [AMBER] Developing Parameters using tleap Brittany Boykin
- [AMBER] Determining number of molecules from a point by integration using xmgrace Sylvester Tumusiime
- Re: [AMBER] Determining number of molecules from a point by integration using xmgrace hannes.loeffler.stfc.ac.uk
- [AMBER] Regarding high temp simulation of DNA and amber MD module MOHD HOMAIDUR RAHMAN
- Re: [AMBER] MCPB.py issues David Poole
- [AMBER] Problem with covalently bonded ligand parametrization Gustavo Avelar Molina
Saturday, 23 May 2015
- Re: [AMBER] Regarding high temp simulation of DNA and amber MD module Carlos Simmerling
- [AMBER] tleap maintainer Matt Harvey
- Re: [AMBER] Developing Parameters using tleap David A Case
- Re: [AMBER] Regarding high temp simulation of DNA and amber MD module David A Case
- Re: [AMBER] Problem with covalently bonded ligand parametrization David A Case
- Re: [AMBER] tleap maintainer David A Case
- Re: [AMBER] Problem with covalently bonded ligand parametrization Gustavo Avelar Molina
- [AMBER] Doubt about ligand binding in proteins Gustavo Avelar Molina
Sunday, 24 May 2015
- [AMBER] cpptraj: lie George Tzotzos
- Re: [AMBER] cpptraj: lie Jason Swails
- [AMBER] NTX Keyword Robert Molt
- Re: [AMBER] cpptraj: lie Daniel Roe
- Re: [AMBER] Doubt about ligand binding in proteins Kenneth Huang
- Re: [AMBER] NTX Keyword Kenneth Huang
- Re: [AMBER] NTX Keyword Jason Swails
Monday, 25 May 2015
- [AMBER] help me to understand using GLYCAM!!! Chris
- [AMBER] Extracting temperature-based potential energies from REMD Lee-Ping Wang
- Re: [AMBER] Extracting temperature-based potential energies from REMD Jason Swails
- Re: [AMBER] Extracting temperature-based potential energies from REMD Lee-Ping Wang
- Re: [AMBER] help me to understand using GLYCAM!!! Lachele Foley
- Re: [AMBER] Extracting temperature-based potential energies from REMD Hai Nguyen
- Re: [AMBER] help me to understand using GLYCAM!!! Chris
- Re: [AMBER] Extracting temperature-based potential energies from REMD Lee-Ping Wang
Tuesday, 26 May 2015
- [AMBER] Protein-Membrane assembly Ofir Tal
- Re: [AMBER] help me to understand using GLYCAM!!! David A Case
- [AMBER] partition error in shake Evgenia Dueva
- Re: [AMBER] partition error in shake David A Case
- Re: [AMBER] MCPB.py issues Pengfei Li
- Re: [AMBER] help me to understand using GLYCAM!!! Lachele Foley
- [AMBER] MMGBSA: pairwise decomposition George Tzotzos
- Re: [AMBER] MMGBSA: pairwise decomposition Jason Swails
- [AMBER] membrane protein simulation Victor Ma
- [AMBER] Next AMBER release? Mohd Farid Ismail
- Re: [AMBER] membrane protein simulation Ross Walker
- Re: [AMBER] Next AMBER release? Ross Walker
Wednesday, 27 May 2015
- [AMBER] RNA unfolding studies.. Asmita Gupta
- [AMBER] loading molecule in leap jacob wick
- Re: [AMBER] RNA unfolding studies.. David A Case
- Re: [AMBER] loading molecule in leap David A Case
- [AMBER] WARNING: SGFT, instead of TEMPSG, should be set for SGMDfp/SGLDfp! barbara rossi
- Re: [AMBER] Arsenic force field parametrization Pengfei Li
- Re: [AMBER] membrane protein simulation Victor Ma
- Re: [AMBER] membrane protein simulation Ross Walker
- Re: [AMBER] Arsenic force field parametrization Jason Swails
- Re: [AMBER] membrane protein simulation Victor Ma
- [AMBER] Fwd: Using the CHARMM force field to run simulations with AMBER Shalini Gupta
- [AMBER] Bug in LIE action command of cpptraj? Samuel Bowerman
- Re: [AMBER] Bug in LIE action command of cpptraj? Jason Swails
- Re: [AMBER] Bug in LIE action command of cpptraj? Samuel Bowerman
- Re: [AMBER] Bug in LIE action command of cpptraj? Jason Swails
- Re: [AMBER] Fwd: Using the CHARMM force field to run simulations with AMBER Jason Swails
- Re: [AMBER] Fwd: Using the CHARMM force field to run simulations with AMBER Brian Radak
- Re: [AMBER] Bug in LIE action command of cpptraj? Samuel Bowerman
- [AMBER] AMBER 15 ERROR 汪盛
- Re: [AMBER] AMBER 15 ERROR Hai Nguyen
- Re: [AMBER] AMBER 15 ERROR Ye Mei
- Re: [AMBER] Fwd: Using the CHARMM force field to run simulations with AMBER hannes.loeffler.stfc.ac.uk
Thursday, 28 May 2015
- [AMBER] Torsion restraints with pmemd.amoeba Karl Debiec
- Re: [AMBER] Torsion restraints with pmemd.amoeba David A Case
- [AMBER] mmpbsa.py.MPI: patching George Tzotzos
- Re: [AMBER] mmpbsa.py.MPI: patching Kenneth Huang
Friday, 29 May 2015
- [AMBER] MMPBSA.py API AttributeError: 'MMPBSA_App' object has no attribute ‘using_chamber' D.J. Pattinson
- Re: [AMBER] MMPBSA.py API AttributeError: 'MMPBSA_App' object has no attribute ‘using_chamber' Jason Swails
- [AMBER] Ambertools 12 Download xy21hb
- Re: [AMBER] Ambertools 12 Download Jason Swails
- Re: [AMBER] Ambertools 12 Download Jason Swails
- Re: [AMBER] Ambertools 12 Download xy21hb
- Re: [AMBER] MMPBSA.py API AttributeError: 'MMPBSA_App' object has no attribute ‘using_chamber' D.J. Pattinson
- Re: [AMBER] Ambertools 12 Download Jason Swails
- [AMBER] Umbrella Sampling and wham MOHD HOMAIDUR RAHMAN
- Re: [AMBER] Arsenic force field parametrization Pengfei Li
- [AMBER] Fwd: MPI Runtime Error Kusum Mehla
Saturday, 30 May 2015
- Re: [AMBER] Fwd: MPI Runtime Error David A Case
- [AMBER] water bridges Hector A. Baldoni
- Re: [AMBER] Umbrella Sampling and wham Brian Radak
- Re: [AMBER] water bridges Sylvester Tumusiime
Sunday, 31 May 2015
- Re: [AMBER] Extracting temperature-based potential energies from REMD Lee-Ping Wang
- Re: [AMBER] Extracting temperature-based potential energies from REMD Hai Nguyen

Last message date: Sun May 31 2015 - 06:30:02 PDT
Archived on: Mon Apr 22 2024 - 05:55:04 PDT

Amber Archive May 2015 by date