Amber Archive Oct 2003: by date

Wednesday, 1 October 2003
- Re: AMBER: improper ya ya
- Re: Re: AMBER: nstlim uddhavesh bhaskar sonavane
- Re: Re: AMBER: nstlim Robert Duke
- Re: AMBER: improper Bill Ross
- AMBER: Added water and mm_pbsa Yong-Liang Zhu
- Re: AMBER: improper Bill Ross
- AMBER: addions/xleap question FyD
- Re: AMBER: addions/xleap question Rhonda Torres
- Re: AMBER: addions/xleap question Bill Ross
- Re: AMBER: addions/xleap question FyD
- AMBER: constant pressure in GB aini.UMDNJ.EDU
- RE: AMBER: constant pressure in GB Yong Duan
Thursday, 2 October 2003
- Re: AMBER: AMBER quasih question(s) David Case
- Re: AMBER: density equilibrium & harmonic restrain David Case
- Re: AMBER: constant pressure in GB David Case
- AMBER: regarding trajectory input and output with ptraj or Carnal Vlad Cojocaru
- Re: AMBER: regarding trajectory input and output with ptraj or Carnal David Case
- AMBER: calculation of LJ 12-6 from .dat file (fwd) Michal Otyepka
- Re: AMBER: regarding trajectory input and output with ptraj or Carnal Bill Ross
- AMBER: SHAKE for TIP4P! Pradipta Bandyopadhyay
Friday, 3 October 2003
- Re: AMBER: SHAKE for TIP4P! David Case
- Re: AMBER: calculation of LJ 12-6 from .dat file (fwd) Martin Lepsik
- Re: AMBER: calculation of LJ 12-6 from .dat file (fwd)-CORRECTION!!! Martin Lepsik
- AMBER: Compiling antechamber on amber 8 Mengjuei Hsieh
- Re: AMBER: Compiling antechamber on amber 8 Junmei Wang
- AMBER: H-bond analysis RAJA SWAMINATHAN
- RE: AMBER: H-bond analysis myang
- AMBER: ibelly Amber Administration
- Re: AMBER: Compiling antechamber on amber 8 Mengjuei Hsieh
Sunday, 5 October 2003
- AMBER: surface code in Amber John Lee
Monday, 6 October 2003
- AMBER: output frequency GUILLERMINA L ESTIU
- RE: AMBER: output frequency Yong Duan
Tuesday, 7 October 2003
- AMBER: mgbjsb Radii in GBSA Giulio Rastelli
- AMBER: Atomic charges and internal H-bond Martin Lepsik
- Re: AMBER: Atomic charges and internal H-bond Jiri Sponer
- Re: AMBER: Atomic charges and internal H-bond Piotr Cieplak
- AMBER: Re:atomic charges and internal H-bond Pradipta Bandyopadhyay
- AMBER: Resp Problem Vikas Varshney
- Re: AMBER: Re:atomic charges and internal H-bond Jiri Sponer
- Re: AMBER: Re:atomic charges and internal H-bond Piotr Cieplak
- Re: AMBER: Re:atomic charges and internal H-bond Jiri Sponer
Wednesday, 8 October 2003
- Re: AMBER: Atomic charges and internal H-bond Martin Lepsik
- AMBER: Addles Mark K. Dean
- Re: AMBER: Addles xiaolin cheng
- AMBER: mopac lil.umbi.umd.edu
- Re: AMBER: mopac Junmei Wang
Thursday, 9 October 2003
- AMBER: Compiling AMBER franck
- AMBER: question about ewald Lishan Yao
- Re: AMBER: question about ewald Scott Brozell
- Re: AMBER: question about ewald darden
- AMBER: mm_pbsa example Jory Zmuda
- Re: AMBER: mm_pbsa example Rhonda Torres
- Re: AMBER: Compiling AMBER, ie, number of atoms limit Scott Brozell
- AMBER: Not getting restrt file on running sanders Vikas Varshney
- RE: AMBER: Not getting restrt file on running sanders Asim Okur
- Re: AMBER: Compiling AMBER, ie, number of atoms limit Robert Duke
- RE: AMBER: Not getting restrt file on running sanders Scott Brozell
- AMBER: Freezing the residues Vikas Varshney
Friday, 10 October 2003
- Re: AMBER: Freezing the residues zhaoxc.puccini.che.pitt.edu
- AMBER: is there a good program to quantitatively analyze hydration effect? zhaoxc.puccini.che.pitt.edu
- AMBER: monte carlo Vlad Cojocaru
- Re: AMBER: monte carlo Andreas Svrcek-Seiler
- AMBER: input/output error Dalmaris, John
- Re: AMBER: Freezing the residues Scott Brozell
- Re: AMBER: Freezing the residues Bill Ross
- Re: AMBER: input/output error Scott Brozell
- AMBER: nmanal projection Qiang Lu
- Re: AMBER: surface code in Amber Alexey Onufriev
- AMBER: MeCNBOX & EWALD bomb northrop.chem.ucla.edu
- Re: AMBER: MeCNBOX & EWALD bomb Jiten
Saturday, 11 October 2003
- AMBER: Water as part of protein in mm_pbsa calculation Yong-Liang Zhu
Sunday, 12 October 2003
- AMBER: force field for hybrid systems Ioana Cozmuta
- AMBER: problem with pdb files Mithun Mitra
- AMBER: sander: vlimit problem Vikas Varshney
Monday, 13 October 2003
- Re: AMBER: problem with pdb files Vlad Cojocaru
- AMBER: Re:mm_pbsa problem Itziar Maestre Asenjo
- AMBER: Reverse TI run Martin Lepsik
- Re: AMBER: problem with pdb files Bill Ross
- AMBER: mm_pbsa crg file kbyun.wesleyan.edu
- AMBER: mm_pbsa rna/dna charges kbyun.wesleyan.edu
- AMBER: antechamber lil.umbi.umd.edu
- Re: AMBER: antechamber Bill Ross
- AMBER: Amber charge problem Yuhui Cheng
- Re: AMBER: Amber charge problem Bill Ross
Tuesday, 14 October 2003
- Re: AMBER: Reverse TI run Martin Lepsik
- AMBER: running sander_classic on multiple processors Richard Smith
- Re: AMBER: mm_pbsa crg file kbyun.wesleyan.edu
- AMBER: mm_pbsa with amber7 Itziar Maestre Asenjo
- AMBER: infinitely long DNA & moil-view? Endres, Robert G.
- Re: AMBER: infinitely long DNA & moil-view? Carlos Simmerling
- Re: AMBER: infinitely long DNA & moil-view? bishop
- AMBER: 'vlimit exceeded' Vikas Varshney
- RE: AMBER: infinitely long DNA & moil-view? Yong Duan
- RE: AMBER: infinitely long DNA & moil-view? Bill Ross
- Re: AMBER: nmanal projection David A. Case
- Re: AMBER: MeCNBOX & EWALD bomb David A. Case
- Re: AMBER: sander: vlimit problem David A. Case
- Re: AMBER: sander: vlimit problem Bill Ross
- AMBER: tru64 alpha Mu Yuguang (Dr)
- AMBER: Restraints to maintain base pair planarity Mahadevan Seetharaman
Wednesday, 15 October 2003
- RE: AMBER: tru64 alpha Mu Yuguang (Dr)
- AMBER: a problem with xleap Ye Mei
- Re: AMBER: Reverse TI run Michael Crowley
- AMBER: STREAM problems : segmentation fault with CARNAL Jean-François Taly
- Re: AMBER: Restraints to maintain base pair planarity David A. Case
- Re: AMBER: tru64 alpha David A. Case
- Re: AMBER: a problem with xleap David A. Case
- RE: AMBER: tru64 alpha Bill Ross
- Re: AMBER: Restraints to maintain base pair planarity Andreas Svrcek-Seiler
- RE: AMBER: running sander_classic on multiple processors Richard Smith
- Re: Re: AMBER: a problem with xleap Ye Mei
- Re: AMBER: tru64 alpha Robert Duke
- RE: AMBER: tru64 alpha Mu Yuguang (Dr)
- Re: AMBER: tru64 alpha Robert Duke
Thursday, 16 October 2003
- Re: AMBER: tru64 alpha Robert Duke
- AMBER: charmm force field in amber Hyonseok Hwang
- Re: AMBER: a problem with xleap Scott Brozell
- Re: AMBER: a problem with xleap Bill Ross
- RE: AMBER: charmm force field in amber myang
- RE: AMBER: tru64 alpha Mu Yuguang (Dr)
- Re: AMBER: tru64 alpha Robert Duke
- Re: AMBER: tru64 alpha Robert Duke
- RE: AMBER: tru64 alpha Mu Yuguang (Dr)
- RE: AMBER: tru64 alpha Yong Duan
- RE: AMBER: tru64 alpha Mu Yuguang (Dr)
- Re: AMBER: tru64 alpha Robert Duke
Friday, 17 October 2003
- RE: AMBER: tru64 alpha Yong Duan
- AMBER: problem in tleap aini.UMDNJ.EDU
- AMBER: Implicit precision in sander vs architecture Teletchéa Stéphane
- Re: AMBER: problem in tleap David A. Case
- Re: AMBER: Implicit precision in sander vs architecture David A. Case
- Re: AMBER: Implicit precision in sander vs architecture Teletchéa Stéphane
- RE: AMBER: Implicit precision in sander vs architecture Yong Duan
- Re: AMBER: Implicit precision in sander vs architecture David E. Konerding
- Re: AMBER: Implicit precision in sander vs architecture Bill Ross
- AMBER: a question Pingna Xu
- AMBER: ibelly in AMBER 6 Qing Zhang
- Re: AMBER: a question David A. Case
- Re: AMBER: ibelly in AMBER 6 David A. Case
Saturday, 18 October 2003
- Re: AMBER: ibelly in AMBER 6 David A. Case
- AMBER: one more question Pingna Xu
- RE: AMBER: one more question myang
Sunday, 19 October 2003
- AMBER: torsional restraints for groups of atoms Samy Name_removed_after_user_request
- AMBER: carnal Frederico.Miranda.ibmb.uib.no
- RE: AMBER: carnal Yong Duan
- AMBER: more questions about igb Pingna Xu
Monday, 20 October 2003
- Re: AMBER: Implicit precision in sander vs architecture Teletchéa Stéphane
- Re: AMBER: Implicit precision in sander vs architecture Robert Duke
- AMBER: stable protein Do Anh Tuan
- Re: AMBER: stable protein Carlos Simmerling
- Re: AMBER: Implicit precision in sander vs architecture Amber Administration
- Re: AMBER: more questions about igb David A. Case
- Re: AMBER: Implicit precision in sander vs architecture David A. Case
- Re: AMBER: Implicit precision in sander vs architecture Robert Duke
- AMBER: what is the unit for the energy calculated from MM_PBSA? zhaoxc.puccini.che.pitt.edu
- RE: AMBER: what is the unit for the energy calculated from MM_PBSA? Rhonda Torres
- AMBER: ECC vs non-ECC (non-amber issue) Yong Duan
- Re: AMBER: ECC vs non-ECC (non-amber issue) Robert Duke
- AMBER: memory SC45 Mu Yuguang (Dr)
- Re: AMBER: memory SC45 Robert Duke
- Re: AMBER: memory SC45 Bill Ross
- RE: AMBER: memory SC45 Mu Yuguang (Dr)
- RE: AMBER: memory SC45 Bill Ross
Tuesday, 21 October 2003
- Re: AMBER: Implicit precision in sander vs architecture Teletchéa Stéphane
- Re: AMBER: memory SC45 Robert Duke
- Re: AMBER: memory SC45 Robert Duke
- AMBER: how to mend the peptide with missing residues? Ye Mei
- RE: AMBER: how to mend the peptide with missing residues? Yong Duan
- AMBER: frozen x unfrozen Herbert Georg
- Re: AMBER: frozen x unfrozen Bill Ross
- RE: AMBER: memory SC45 Mu Yuguang (Dr)
- Re: AMBER: memory SC45 Robert Duke
Wednesday, 22 October 2003
- AMBER: antechamber and bond type Herbert Georg
- Re: AMBER: frozen x unfrozen David A. Case
- Re: AMBER: torsional restraints for groups of atoms David A. Case
- Re: AMBER: torsional restraints for groups of atoms xiaolin cheng
Thursday, 23 October 2003
- Re: AMBER: frozen x unfrozen Herbert Georg
- AMBER: Simulation of small protein Endres, Robert G.
- AMBER: frozen x unfrozen and the gibbs tragedy David Smith
- Re: AMBER: Simulation of small protein Carlos Simmerling
- RE: AMBER: Simulation of small protein Endres, Robert G.
- AMBER: correlated motion Jory L. Zmuda
Friday, 24 October 2003
- AMBER: Simulation of small protein (MD Display tips) Chris Moth
Thursday, 23 October 2003
- AMBER: mddisplay Samy Name_removed_after_user_request
Friday, 24 October 2003
- AMBER: mddisplay Chris Moth
Thursday, 23 October 2003
- AMBER: SHAKE question Herbert Georg
- Re: AMBER: SHAKE question Bill Ross
- Re: AMBER: Simulation of small protein Carlos Simmerling
- RE: AMBER: Simulation of small protein Yong Duan
- RE: AMBER: Simulation of small protein Endres, Robert G.
- RE: AMBER: Simulation of small protein Yong Duan
Friday, 24 October 2003
- AMBER: carnal iteration deviation from original crd file Dalmaris, John
- Re: AMBER: carnal iteration deviation from original crd file Vlad Cojocaru
- RE: AMBER: carnal iteration deviation from original crd file Dalmaris, John
- Re: AMBER: carnal iteration deviation from original crd file Vlad Cojocaru
- Re: AMBER: carnal iteration deviation from original crd file aini.UMDNJ.EDU
- AMBER: prmtop file format Herbert Georg
- RE: AMBER: prmtop file format Yong Duan
- Re: AMBER: carnal iteration deviation from original crd file Bill Ross
- RE: AMBER: carnal iteration deviation from original crd file Bill Ross
- AMBER: Pressure in NVT ensemble Shiang-Tai Lin
- Re: AMBER: prmtop file format Herbert Georg
- RE: AMBER: prmtop file format Yong Duan
- Re: AMBER: problem in tleap aini.UMDNJ.EDU
- Re: AMBER: problem in tleap Scott Brozell
Saturday, 25 October 2003
- AMBER: RMSD and Radius of Gyration Endres, Robert G.
- Re: AMBER: RMSD and Radius of Gyration Carlos Simmerling
- RE: AMBER: RMSD and Radius of Gyration Yong Duan
- Re: AMBER: antechamber and bond type David A. Case
- Re: AMBER: Pressure in NVT ensemble David A. Case
- Re: AMBER: problem in tleap David A. Case
- AMBER: MD simulation: enzyme and its substrate Do Anh Tuan
Sunday, 26 October 2003
- Re[2]: AMBER: surface code in Amber John Lee
- Re: AMBER: surface code in Amber David A. Case
Monday, 27 October 2003
- AMBER: comparing versions 6.0 and 7.0 of AMBER Therese Malliavin
- AMBER: amber 7 for industrial application Jose Gallego
- AMBER: solute images Sandro Fornili
- Re: AMBER: surface code in Amber David E. Konerding
- Re: AMBER: Pressure in NVT ensemble Shiang-Tai Lin
- AMBER: Implicit MD simulations in Amber7 Joey Harriman
- Re: AMBER: Implicit MD simulations in Amber7 Scott Brozell
- Re: AMBER: solute images Scott Brozell
- AMBER: Removal of Rotational and Translational Motion in AMBER6 Richard Smith
- AMBER: aminoacid mutation Ioana Cozmuta
- RE: AMBER: carnal iteration deviation from original crd file John
- AMBER: SC45 Mu Yuguang (Dr)
- RE: AMBER: aminoacid mutation Yong Duan
- RE: AMBER: aminoacid mutation Endres, Robert G.
Tuesday, 28 October 2003
- AMBER: Radius of Gyration and RMSD Jagannadh B
Monday, 27 October 2003
- RE: AMBER: aminoacid mutation Bill Ross
- AMBER: aminoacid mutation Wayne Dawson
- Re: AMBER: amber 7 for industrial application David A. Case
- Re[2]: AMBER: surface code in Amber John Lee
Tuesday, 28 October 2003
- Re[2]: AMBER: surface code in Amber Dr. Yong Duan
- RE: AMBER: Radius of Gyration and RMSD Endres, Robert G.
- RE: AMBER: amber 7 for industrial application Jose Gallego
- RE: AMBER: aminoacid mutation Sivakolundu, Sivashankar
- RE: AMBER: amber 7 for industrial application Junmei Wang
- Re: AMBER: surface code in Amber David E. Konerding
- RE: AMBER: surface code in Amber Yong Duan
- AMBER: how to measure the minor groove widths of a DNA? zhaoxc.puccini.che.pitt.edu
- RE: AMBER: Radius of Gyration and RMSD Bill Ross
- AMBER: ibelly problem Vikas Varshney
- Re: AMBER: how to measure the minor groove widths of a DNA? Peter Gannett
- RE: AMBER: aminoacid mutation Ioana Cozmuta
- Re: AMBER: aminoacid mutation Osmar Norberto de Souza
- Re: AMBER: aminoacid mutation Amber Administration
- AMBER: Installation Problem, xleap can't load pdb files Jonathan Neidigh
- Re: AMBER: surface code in Amber David A. Case
- AMBER: mddisplay Samy Name_removed_after_user_request
- RE: AMBER: mddisplay Kristina Furse
Wednesday, 29 October 2003
- Re: AMBER: Installation Problem, xleap can't load pdb files Jonathan Neidigh
- RE: AMBER: amber 7 for industrial application Bayly, Christopher
- Re: AMBER: ibelly problem Thomas E. Cheatham, III
- Re: AMBER: how to measure the minor groove widths of a DNA? Thomas E. Cheatham, III
Thursday, 30 October 2003
- AMBER: mddisplay Chris Moth
Wednesday, 29 October 2003
- AMBER: reduce box and delete excess solvent Endres, Robert G.
- AMBER: MD simulation: enzyme and its substrate Do Anh Tuan
- Re: AMBER: MD simulation: enzyme and its substrate!! Pradipta Bandyopadhyay
- AMBER: JAC on NCSA titan (Itanium 2 833MHZ) Qiang Lu
Thursday, 30 October 2003
- AMBER: wangf2
- Re: AMBER: David A. Case
- Re: AMBER: minimize a covalently bounded protein-ligand complex David A. Case
- AMBER: minimize a covalently bounded protein-ligand complex Eric Hu
Friday, 31 October 2003
- AMBER: PMEMD 3.1 Release - High Scalability Update to PMEMD Robert Duke
- Re: AMBER: What does this error message mean? Ioana Cozmuta
- AMBER: What does this error message mean? nie beining
- Re: AMBER: What does this error message mean? Jose Ramon Blas
- Re: AMBER: What does this error message mean? nie beining
Saturday, 4 October 2003
- AMBER: large file for carnal volodya
Sunday, 5 October 2003
- Re: AMBER: large file for carnal volodya
Tuesday, 7 October 2003
- Re: AMBER: large file for carnal volodya
- AMBER: RMSd per residue volodya
Sunday, 12 October 2003
- Re: AMBER: Protein Rotation volodya

Last message date: Tue Nov 11 2003 - 14:53:01 PST
Archived on: Fri Oct 31 2025 - 05:53:20 PDT

Amber Archive Oct 2003 by date