Amber Archive Mar 2006: by date

Tuesday, 28 February 2006
- Re: AMBER: How to develop charge for my deprotonated glycine FyD
Wednesday, 1 March 2006
- AMBER: install error biolabadmin.ibt.lt
- AMBER: Nmode vs QM Freq Calculation Mark Williamson
- AMBER: leap: syntax error when use source command Dmitry Osolodkin
- RE:AMBER: leap: syntax error when use source command Kateryna Miroshnychenko
- RE: AMBER: install error Ross Walker
- AMBER: replica exchange hangs Peter Varnai
- Re: AMBER: replica exchange hangs Sergey Krishtal
- Re: AMBER: replica exchange hangs Carlos Simmerling
- Re: AMBER: replica exchange hangs Carlos Simmerling
- Re: AMBER: Nmode vs QM Freq Calculation David A. Case
- Re: AMBER: replica exchange hangs Peter Varnai
- Re: AMBER: failed to save prm and xyz using ff96 Joseph Nachman
- AMBER: GAFF + AM1BCC & small-molecule aggregation Scott P Brown
- Re: AMBER: failed to save prm and xyz using ff96 Viktor Hornak
- Re: AMBER: GAFF + AM1BCC & small-molecule aggregation Thomas E. Cheatham, III
- Re: AMBER: GAFF + AM1BCC & small-molecule aggregation Carlos Simmerling
- Re: AMBER: failed to save prm and xyz using ff96 Joseph Nachman
- Re: AMBER: GAFF + AM1BCC & small-molecule aggregation Carlos Simmerling
- AMBER: N-H and C-H Residual Dipolar Coupling thenmalar
- Re: AMBER: N-H and C-H Residual Dipolar Coupling David A. Case
- Re: AMBER: N-H and C-H Residual Dipolar Coupling thenmalar
- AMBER: Amber 9. Sergey Krishtal
- AMBER: Which PTRAJ distribution to use? Chng Choon-Peng
Thursday, 2 March 2006
- Re: AMBER: install error biolabadmin.ibt.lt
- AMBER: transition metals and the parmcal of the antechamber module Cenk Andac
- Re: AMBER: install error Mark Williamson
- AMBER: amber8 and gfortran 4.1.0 Tru Huynh
- RE: AMBER: amber8 and gfortran 4.1.0 Ross Walker
- Re: AMBER: amber8 and gfortran 4.1.0 Andreas Svrcek-Seiler
- Re: AMBER: amber8 and gfortran 4.1.0 Tru Huynh
- Re: AMBER: amber8 and gfortran 4.1.0 Tru Huynh
- Re: AMBER: amber8 and gfortran 4.1.0 David A. Case
- AMBER: AMBER 8 VS AMBER 7 venditti2.unisi.it
- Re: AMBER: AMBER 8 VS AMBER 7 David A. Case
- Re: AMBER: AMBER 8 VS AMBER 7 Carlos Simmerling
- RE: AMBER: generating parameters for the NADH analogue H4NAD Simon Whitehead
- RE: AMBER: generating parameters for the NADH analogue H4NAD Ross Walker
- Re: AMBER: Which PTRAJ distribution to use? Thomas Cheatham
- Re: AMBER: Which PTRAJ distribution to use? Chng Choon-Peng
- AMBER: G95, SGI and Amber8 Cenk Andac
Friday, 3 March 2006
- Re: AMBER: install error biolabadmin.ibt.lt
- AMBER: about Br- parameters JAVIER PEREZ
- Re: AMBER: about Br- parameters Vitor Manuel Sousa F?x
- Re: AMBER: about Br- parameters german
- Re: AMBER: about Br- parameters Shulin Zhuang
- Re: AMBER: about Br- parameters Mathy Froeyen
- Re: AMBER: about Br- parameters Vitor Manuel Sousa F?x
- Re: AMBER: Amber 9. David A. Case
- AMBER: from Wei Zhang: flight information Wei Zhang
- Re: AMBER: How to develop charge for my deprotonated glycine Jianzhong Liu
Saturday, 4 March 2006
- Re: AMBER: How to develop charge for my deprotonated glycine FyD
- Re: AMBER: How to develop charge for my deprotonated glycine Jianzhong Liu
Sunday, 5 March 2006
- AMBER: sander restart problem Vlad Cojocaru
- AMBER: charge neutralization with GB Manish Datt
- AMBER: ptraj:hbond question Yam
Monday, 6 March 2006
- AMBER: how to calculate the RMSD and B-factor for all atoms of residue haixiao jin
- Re: AMBER: how to calculate the RMSD and B-factor for all atoms of residue Chng Choon-Peng
- AMBER: the total energy is not converge as the cutoff increase thanyarat Udom
- Re: AMBER: the total energy is not converge as the cutoff increase Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini)
- Re: AMBER: the total energy is not converge as the cutoff increase Cenk Andac
- RE: AMBER: the total energy is not converge as the cutoff increase Ross Walker
- AMBER: How to patch the configure script (macosx) K. Yarem
- Re: AMBER: sander restart problem Melinda Layten
- Re: AMBER: How to patch the configure script (macosx) David A. Case
- AMBER: Problem taking the PDB to the Amber coordinates for calculations Brian Stupi
- Re: AMBER: Problem taking the PDB to the Amber coordinates for calculations Ilyas Yildirim
- Re: AMBER: Problem taking the PDB to the Amber coordinates for calculations Thomas Cheatham
- AMBER: Different results between serial and parallel runs in AMBER 8 Ilyas Yildirim
- AMBER: rms processing A D
- Re: AMBER: rms processing Ilyas Yildirim
- Re: AMBER: Different results between serial and parallel runs in AMBER 8 Carlos Simmerling
- Re: AMBER: Different results between serial and parallel runs in AMBER 8 David A. Case
- AMBER: h bond analysis Claire Zerafa
- AMBER: Amber 8 under Solaris 9 compilation failed Dror
- AMBER: Amber 8 under Solaris 9 compilation failed Dror
- RE: AMBER: the total energy is not converge as the cutoff increase thanyarat Udom
Tuesday, 7 March 2006
- AMBER: ptraj: hbond analysis Yam
- Re: AMBER: how to calculate the RMSD and B-factor for all atoms of residue haixiao jin
- Re: AMBER: Different results between serial and parallel runs in AMBER 8 Ilyas Yildirim
- Re: AMBER: Different results between serial and parallel runs in AMBER 8 Ilyas Yildirim
- Re: AMBER: Different results between serial and parallel runs in AMBER 8 David A. Case
- Re: AMBER: Different results between serial and parallel runs in AMBER 8 David A. Case
- Re: AMBER: Amber 8 under Solaris 9 compilation failed David A. Case
- Re: AMBER: Problem taking the PDB to the Amber coordinates for calculations Brian Stupi
- Re: AMBER: Problem taking the PDB to the Amber coordinates for calculations David A. Case
- Re: AMBER: Problem taking the PDB to the Amber coordinates for calculations Brian Stupi
- AMBER: Trouble with combining a non-standard residue with a protein of standard residue Nitin Bhardwaj
- AMBER: question about solvatecap commander aini.umdnj.edu
- Re: AMBER: question about solvatecap commander mfyang
- Re: AMBER: question about solvatecap commander David A. Case
- AMBER:molsurf: molsurf.c:1057: is_buried: Assertion `sarg1 >= 0.0' failed snowyowls
Wednesday, 8 March 2006
- AMBER: NADP(H) parameters Simon Whitehead
- AMBER: Dror
- AMBER: converting .lib files Simon Whitehead
- AMBER: Cosine content calculation matteo filandri
- Re: AMBER: converting .lib files David A. Case
- Re: AMBER: NADP(H) parameters David A. Case
- Re: AMBER: converting .lib files Bill Ross
- Re: AMBER:molsurf: molsurf.c:1057: is_buried: Assertion `sarg1 >= 0.0' failed David A. Case
- Re: AMBER: Cosine content calculation David A. Case
- AMBER: modeling a non-standard molecule. Nitin Bhardwaj
- Re: AMBER: modeling a non-standard molecule. Bill Ross
- Re: AMBER: modeling a non-standard molecule. Nitin Bhardwaj
- Re: AMBER: modeling a non-standard molecule. Bill Ross
- AMBER: aligning polymer with Z-axis of periodic box Kenley Barrett
- Re: AMBER: aligning polymer with Z-axis of periodic box Ilyas Yildirim
- Re: AMBER: aligning polymer with Z-axis of periodic box Kenley Barrett
- AMBER: bond parameters for positively charged guanidine group Ye Mei
- AMBER: prepin format nkyx.sohu.com
- AMBER: MD and MMPBSA alexandra.marques.fc.up.pt
- RE: AMBER: MD and MMPBSA Ross Walker
- Re: AMBER: Trouble with combining a non-standard residue with a protein of standard residue FyD
- Re: AMBER: bond parameters for positively charged guanidine group Ilyas Yildirim
- Re: Re: AMBER: bond parameters for positively charged guanidine group Ye Mei
- Re: Re: AMBER: bond parameters for positively charged guanidine group Ilyas Yildirim
Thursday, 9 March 2006
- Re: Re: AMBER: bond parameters for positively charged guanidine group FyD
- Re: Re: Re: AMBER: bond parameters for positively charged guanidine group Ye Mei
- Re: AMBER: Cosine content calculation matteo filandri
- AMBER: CPU utilization with Parallel Sander Jingyuan Luke
- RE: AMBER: CPU utilization with Parallel Sander Ross Walker
- Re: AMBER: Cosine content calculation David A. Case
- Re: Re: Re: AMBER: bond parameters for positively charged guanidine group Bill Ross
- AMBER: RE: hi & question Ross Walker
- AMBER: Power Mac G5 Shuting Wei
- Re: AMBER: Power Mac G5 David A. Case
- Re: AMBER: Cosine content calculation Hannes Loeffler
- Re: AMBER: prepin format David A. Case
Friday, 10 March 2006
- AMBER: Antechamber calculations Varsha Goyal
- Re: AMBER: Antechamber calculations Vitor Manuel Sousa F?x
- Re: AMBER: Antechamber calculations Varsha Goyal
- AMBER: error while running sander snoze pa
- Re: AMBER: error while running sander Thomas Cheatham
Saturday, 11 March 2006
- AMBER: Input conversion error. Sergey Krishtal
- Re: Re: Re: Re: AMBER: bond parameters for positively charged guanidine group Ye Mei
- Re: Re: Re: Re: AMBER: bond parameters for positively charged guanidine group Bill Ross
- AMBER: divalent ions Ioana Cozmuta
- Re: AMBER: Input conversion error. Carlos Simmerling
- AMBER: using MM_PBSA just for binding site, feasible ??? tonglei
Monday, 13 March 2006
- AMBER: Suitable water box simon whitehead
- AMBER: amber 8 install problem qiwenpeng.sinap.ac.cn
- AMBER: Steve Seibold
- Re[2]: AMBER: Input conversion error. Sergey Krishtal
- Re: AMBER: Suitable water box Jianzhong Liu
- AMBER: NTT for production run snoze pa
- Re: AMBER: David A. Case
- Re: AMBER: amber 8 install problem David A. Case
- Re: AMBER: Ilyas Yildirim
Tuesday, 14 March 2006
- Re: AMBER: NTT for production run Vlad Cojocaru
- AMBER: Xleap 64 bit installation problem Cenk Andac
- Re: AMBER: Xleap 64 bit installation problem Andreas Svrcek-Seiler
- AMBER: nucgen error bala
- Re: AMBER: nucgen error Bill Ross
- AMBER: divalent ions Ioana Cozmuta
- Re: AMBER: divalent ions Thomas E. Cheatham, III
- AMBER: quistions about pbsa cacultaion snowyowls
- Re: AMBER: NTT for production run David A. Case
- Re: AMBER: Xleap 64 bit installation problem David A. Case
Sunday, 12 March 2006
- Re: AMBER: quistions about pbsa cacultaion Ray Luo
Tuesday, 14 March 2006
- Re: AMBER: quistions about pbsa cacultaion snowyowls
Wednesday, 15 March 2006
- Re: AMBER: NTT for production run Vlad Cojocaru
- Re: AMBER: amber 8 install problem qiwenpeng.sinap.ac.cn
- RE: AMBER: NTT for production run Ross Walker
- AMBER: k-space cutoff with standard Ewald Guowen
- Re: AMBER: NTT for production run snoze pa
- Re: AMBER: quistions about pbsa cacultaion Ray Luo
- Re: AMBER: NTT for production run David A. Case
- Re: AMBER: amber 8 install problem David A. Case
- Re: AMBER: amber 8 install problem David A. Case
Thursday, 16 March 2006
- Re: AMBER: NTT for production run Vlad Cojocaru
- AMBER: Zoom Angelo
- Re: AMBER: Zoom Laurent Chiche
- AMBER: mm-pbsa vorasit vongsutilers
- Re: AMBER: Zoom Angelo
- Re: AMBER: Zoom Laurent Chiche
- Re: AMBER: Zoom Angelo
- Re: AMBER: mm-pbsa Holger Gohlke
- Re: AMBER: NTT for production run David A. Case
- AMBER: faulty ambpdb compilation? Benjamin Juhl
- RE: AMBER: faulty ambpdb compilation? Ross Walker
- Re: AMBER: faulty ambpdb compilation? Benjamin Juhl
- AMBER: constant pH simulation Abhilash Mohan
- Re: AMBER: Zoom Ilyas Yildirim
Friday, 17 March 2006
- Re: AMBER: NTT for production run Vlad Cojocaru
- Re: AMBER: mm-pbsa vorasit vongsutilers
- Re: AMBER: mm-pbsa Scott Pendley
- AMBER: prep files for L-sugar residues Qizhi Cui
Sunday, 19 March 2006
- Re: AMBER: dynamic memory allocation problem in nmode Cenk Andac
- AMBER: Ewald and ibelly Austin B. Yongye
- Re: AMBER: mm-pbsa vorasit vongsutilers
- Re: AMBER: Ewald and ibelly David A. Case
Monday, 20 March 2006
- AMBER: emilia wu
- AMBER: energy conservation in NVE ensemble (ntt=0, ntb=1) Vlad Cojocaru
- Re: AMBER: mm-pbsa Scott Pendley
- AMBER: a challenge: a periodic box that cuts through a monomer Kenley Barrett
- Re: AMBER: rms processing Jianyin Shao
- AMBER: anal: dihedral error renyanliang
- Re: AMBER: a challenge: a periodic box that cuts through a monomer David A. Case
- Re: AMBER: David A. Case
Tuesday, 21 March 2006
- AMBER: MMPBSA alexandra.marques.fc.up.pt
- AMBER: heating system snoze pa
- RE: AMBER: heating system Ross Walker
- Re: AMBER: heating system snoze pa
- Re: AMBER: constant pH simulation John Mongan
Wednesday, 22 March 2006
- AMBER: About statistics results in MMPBSA_DC pair 莉张
- RE: AMBER: heating system Ross Walker
- AMBER: Related to RESTRAINT_WT snoze pa
- Re: AMBER: Related to RESTRAINT_WT David A. Case
- Re: AMBER: Related to RESTRAINT_WT Chng Choon-Peng
- AMBER: Solvating the system with specific number of water molecules... Ilyas Yildirim
Thursday, 23 March 2006
- AMBER: about atomic fluctuation & RMSF xueping
- AMBER: question capping helix ends Zhuang
- Re: AMBER: question capping helix ends Vlad Cojocaru
- AMBER: what is unit of the out put of mmpbsa caculation snowyowls
- Re: AMBER: what is unit of the out put of mmpbsa caculation Holger Gohlke
- Re: AMBER: about atomic fluctuation & RMSF Holger Gohlke
- AMBER: Average pdb Claire Zerafa
- RE: AMBER: Average pdb John Jett
- AMBER: question capping helix ends Zhuang
- AMBER: Parmtop file: ANGLE_EQUIL_VALUE actually in radians? amanda.mccook.gatech.edu
- RE: AMBER: Parmtop file: ANGLE_EQUIL_VALUE actually in radians? Ross Walker
Friday, 24 March 2006
- Re: AMBER: question capping helix ends Cenk Andac
- Re: AMBER: question capping helix ends Vlad Cojocaru
- RE: AMBER: heating system Ross Walker
Saturday, 25 March 2006
- Re: AMBER: anal: dihedral error David A. Case
Sunday, 26 March 2006
- AMBER: negative values of PBSOL and PBCAL in mm_pbsa result tonglei
- Re: AMBER: about atomic fluctuation & RMSF xueping
- AMBER: temp control snoze pa
- To dac --AMBER: anal: dihedral error 莉张
- Re: AMBER: Amber 8 under Solaris 9 compilation failed Scott Brozell
Monday, 27 March 2006
- AMBER: OSX 10.4 G4 xlf90 compilation errors K. Yarem
- Re: AMBER: OSX 10.4 G4 xlf90 compilation errors David Case
Tuesday, 28 March 2006
- AMBER: How to give the specific pressure parameter for NTP=2 hbluo
- AMBER: united atoms nadiav.soton.ac.uk
- AMBER: amber8 error installation Abd Ghani Abd Aziz
- Re: AMBER: amber8 error installation Mark Williamson
- Re: AMBER: amber8 error installation Abd Ghani Abd Aziz
- Re: AMBER: amber8 error installation Mark Williamson
- Re: AMBER: amber8 error installation Abd Ghani Abd Aziz
- RE: AMBER: amber8 error installation Ross Walker
- Re: AMBER: united atoms Bill Ross
- AMBER: hessian calculation sebnem
- Re: AMBER: hessian calculation David A. Case
- Re: AMBER: hessian calculation sebnem.mercury.chem.pitt.edu
- AMBER: AMBER : About the kinetic energy and temperature (GBSA model) James W
- Re: AMBER: AMBER : About the kinetic energy and temperature (GBSA model) David A. Case
- Re: AMBER: hessian calculation David A. Case
- RE: AMBER: amber8 error installation John Bushnell
- Re: AMBER: hessian calculation sebnem
- Re: AMBER: hessian calculation sebnem
- AMBER: installation problem r. a.
- Re: AMBER: installation problem Mark Williamson
- Fw: AMBER: AMBER : About the kinetic energy and temperature (GBSA model) James W
- Re: AMBER: installation problem Abd Ghani Abd Aziz
- Re: Fw: AMBER: AMBER : About the kinetic energy and temperature (GBSA model) Thomas Cheatham
- RE: AMBER: AMBER : About the kinetic energy and temperature (GBSA model) Ross Walker
- RE: AMBER: amber8 error installation Ross Walker
- AMBER: Impropers definition egorov
Wednesday, 29 March 2006
- AMBER: Simulating a periodic crystal Jiang Jianwen
- Re: AMBER: Simulating a periodic crystal Thomas Cheatham
- AMBER: Announcement: Amber 9 is now available David A. Case
- Re: AMBER: Impropers definition David A. Case
- Re: AMBER: hessian calculation sebnem.mercury.chem.pitt.edu
- AMBER: Dimer Image Wrapping Melinda Layten
- AMBER: post-processing replica exchange trajectory Zhuang
- Re: AMBER: hessian calculation David A. Case
- AMBER: Problem with setbox command... Ilyas Yildirim
Thursday, 30 March 2006
- Re: AMBER: Problem with setbox command... David A. Case
- AMBER: charge constraints in resp Kenley Barrett
- Re: AMBER: hessian calculation sebnem
- Re: AMBER: charge constraints in resp Ilyas Yildirim
- Re: AMBER: Dimer Image Wrapping Scott Pendley
- Re: AMBER: Dimer Image Wrapping Melinda Layten
- AMBER: Gromos to Amber Ann Vilan Tran
- Re: AMBER: charge constraints in resp Kenley Barrett
- Re: AMBER: charge constraints in resp Ilyas Yildirim
- AMBER: LES error Claudia Steinert
Friday, 31 March 2006
- RE: AMBER: Simulating a periodic crystal Jiang Jianwen
- Re: AMBER: Problem with setbox command... Ilyas Yildirim
- AMBER: Ptraj & pca Claire Zerafa
- AMBER: MMPBSA & PBCAL Rabal Gracia María Obdulia
- Re: AMBER: Announcement: Amber 9 is now available David E. Konerding
- Re: AMBER: Announcement: Amber 9 is now available David A. Case
- Re: AMBER: Announcement: Amber 9 is now available David A. Case
- AMBER: ptraj help - ERROR in readParm: ... failed to find CHARGE fine wu
- Re: AMBER: ptraj help - ERROR in readParm: ... failed to find CHARGE Thomas E. Cheatham, III
- AMBER: chirality.c error in xleap Kenley Barrett
- Re: AMBER: ptraj help - ERROR in readParm: ... failed to find CHARGE Ilyas Yildirim
- Re: AMBER: chirality.c error in xleap David A. Case

Last message date: Sun Apr 02 2006 - 06:10:17 PDT
Archived on: Fri Apr 19 2024 - 05:53:14 PDT

Amber Archive Mar 2006 by date