Amber Archive Sep 2003: by date

Monday, 1 September 2003
- AMBER: processors Herbert Georg
- title card? Re: AMBER: what can't I use ibelly? nie beining
- Re: title card? Re: AMBER: what can't I use ibelly? David A. Case
Tuesday, 2 September 2003
- AMBER: MIPS R14000 and Machine-file Antonio J.Díaz Quintana
- AMBER: MIPS R14000 and Machine-file Antonio J.Díaz Quintana
- Re: AMBER: MIPS R14000 and Machine-file Sanjeev B.S.
- Re: AMBER: MIPS R14000 and Machine-file David A. Case
- AMBER: error message is the same after I added a title nie beining
- AMBER: PMF ethane example: Can someone correct the INPUT? Thanks. Christophe L M J Verlinde
- AMBER: GLYCAM/AMBER Configurator ayongye.sunchem.chem.uga.edu
- AMBER: surften value in mm_gbsa/mm_pbsa calculations Sergio E. Wong
- Re: AMBER: surften value in mm_gbsa/mm_pbsa calculations Holger Gohlke
- AMBER: atomic clash or structure size? atobak.eden.rutgers.edu
- Re: AMBER: atomic clash or structure size? Qiang Lu
Wednesday, 3 September 2003
- Re: AMBER: atomic clash or structure size? David A. Case
- Re: AMBER: PMF ethane example: Can someone correct the INPUT? Thanks. David A. Case
Thursday, 4 September 2003
- Re: AMBER: processors Scott Brozell
- AMBER: charge of IRON in HEME!! Pradipta Bandyopadhyay
- Re: AMBER: charge of IRON in HEME!! Qiang Lu
Friday, 5 September 2003
- AMBER: problems with periodic boundary conditions Monika Fuxreiter
- AMBER: DNA helix is not in z-direction A. Hungie
- AMBER: IG value SEKIJIMA Masakazu
- Re: AMBER: IG value Carlos Simmerling
- Re: AMBER: problems with periodic boundary conditions Michael Crowley
- Re: AMBER: problems with periodic boundary conditions David A. Case
- Re: AMBER: IG value David A. Case
- AMBER: Accuracy of PB solvation energy Qing Zhang
- Re: AMBER: Accuracy of PB solvation energy Jiri Sponer
- AMBER: Using NWCHEM for esp? David E. Konerding DSD Staff
- RE: AMBER: charge of IRON in HEME!! Ming Lei
- AMBER: 'ho' vDW parameters Lee, Matthew
- Re: AMBER: DNA helix is not in z-direction David A. Case
- Re: AMBER: Using NWCHEM for esp? Peter Oelschlaeger
Saturday, 6 September 2003
- AMBER: solvatebox-solvateshell Majid moghaddam
- AMBER: charge definition Khanh KIm Dao
- Re: AMBER: charge definition Holger Gohlke
- Re: AMBER: solvatebox-solvateshell David A. Case
- AMBER: update to answer about solvateShell David A. Case
- Re: AMBER: solvatebox-solvateshell Thomas E. Cheatham, III
Sunday, 7 September 2003
- Re: AMBER: Using NWCHEM for esp? FyD
Monday, 8 September 2003
- AMBER: dielectric constant for blends Taner E. Dirama
- Re: AMBER: dielectric constant for blends David A. Case
- AMBER: parm. and top. for sugars, charmm? Endres, Robert G.
- Re: AMBER: 'ho' vDW parameters Junmei Wang
- Re: AMBER: 'ho' vDW parameters Carlos Simmerling
- RE: AMBER: 'ho' vDW parameters Yong Duan
- Re: AMBER: solvatebox-solvateshell Xavier Periole
- AMBER: Compiling 64-bit version on AIX Pratul K. Agarwal
- Re: AMBER: parm. and top. for sugars, charmm? Itziar Maestre Asenjo
Tuesday, 9 September 2003
- Re: AMBER: Compiling 64-bit version on AIX Nicolas Grima
- AMBER: radial distribution-function by Ptraj Petrodler.aol.com
- AMBER: reporting atoms clashed during simple energy minimization jackie.ibms.sinica.edu.tw
- AMBER: SHAKE poblem with dummy atoms Itziar Maestre Asenjo
- Re: AMBER: reporting atoms clashed during simple energy minimization Dr. Yong Duan
- AMBER: PMF calculations Sébastien Canneaux
- AMBER: TIP5P Ulf Johansson
- Re: AMBER: TIP5P David A. Case
- Re: AMBER: reporting atoms clashed during simple energy minimization David A. Case
- Re: AMBER: SHAKE poblem with dummy atoms David A. Case
- Re: AMBER: Compiling 64-bit version on AIX Pratul K. Agarwal
- Re: AMBER: Compiling 64-bit version on AIX Carlos P. Sosa
- Re: AMBER: Compiling 64-bit version on AIX David A. Case
- Re: AMBER: Compiling 64-bit version on AIX Pratul K. Agarwal
Wednesday, 10 September 2003
- Re: AMBER: TIP5P Ulf Johansson
- Re: AMBER: TIP5P David A. Case
- AMBER: Re: torsional energy David A. Case
Thursday, 11 September 2003
- AMBER: altering mass in .top file hagop demirdjian
- Re: AMBER: altering mass in .top file Pascal Bonnet
- AMBER: EWALD BOMB and solvent density problem northrop.chem.ucla.edu
- AMBER: ptraj question Lishan Yao
Friday, 12 September 2003
- AMBER: gaff parameters astrid.maass
- AMBER: DMSO box Dalmaris, John
- Re: AMBER: gaff parameters Kazuo Koyano
- AMBER: FF parameters for BOC - group Balvinder Singh
- Re: AMBER: FF parameters for BOC - group Martin Lepsik
- AMBER: minimization error Venkata S Koppuravuri
- Re: AMBER: minimization error Scott Brozell
- Re: AMBER: minimization error David A. Case
- Re: AMBER: gaff parameters Junmei Wang
- Re: AMBER: DMSO box Jiten
Sunday, 14 September 2003
- AMBER: AMBER on LINUX ?? (fwd) sangeeta.bioinfo.ernet.in
Monday, 15 September 2003
- Re: AMBER: AMBER on LINUX ?? (fwd) Sanjeev B.S.
- Re: AMBER: AMBER error in CHALANGE Carlos Simmerling
- AMBER: AMBER error in CHALANGE sd233.georgetown.edu
- AMBER: sander on cygwin Lee, Matthew
- Re: AMBER: sander on cygwin David E. Konerding DSD Staff
- AMBER: performance vs number of processors GUILLERMINA L ESTIU
- Re: AMBER: performance vs number of processors zhaoxc.puccini.che.pitt.edu
- Re: AMBER: performance vs number of processors David A. Case
- Re: AMBER: sander on cygwin David A. Case
- Re: AMBER: AMBER error in CHALANGE David A. Case
- Re: AMBER: AMBER on LINUX ?? (fwd) David A. Case
- AMBER: Benchmark of AMBER on Apple G5 machine Mengjuei Hsieh
- Re: AMBER: sander on cygwin David E. Konerding DSD Staff
Tuesday, 16 September 2003
- AMBER: PMEMD: dual XEON vs SGI cluster Chris Moth
Monday, 15 September 2003
- Re: AMBER: PMEMD: dual XEON vs SGI cluster Robert Duke
- Re: AMBER: PMEMD: dual XEON vs SGI cluster Johannes Zuegg
- RE: AMBER: PMEMD: dual XEON vs SGI cluster Chris Moth
Tuesday, 16 September 2003
- AMBER: MD simulations on small molecules immersed in sparse water shell Junmei Wang
- Re: AMBER: MD simulations on small molecules immersed in sparse water shell Alfonso Garcia Sosa
- Re: AMBER: MD simulations on small molecules immersed in sparse water shell rluo.uci.edu
- Re: AMBER: MD simulations on small molecules immersed in sparse water shell Carlos Simmerling
- Re: AMBER: MD simulations on small molecules immersed in sparse water shell rluo.uci.edu
- Re: AMBER: MD simulations on small molecules immersed in sparse water shell Carlos Simmerling
- AMBER: MD problem! Pradipta Bandyopadhyay
- AMBER: Compiling sander with single precision rluo.uci.edu
- Re: AMBER: Compiling sander with single precision Scott Brozell
Wednesday, 17 September 2003
- Re: AMBER: MD problem! darden
- AMBER: mfef90 - installation problem Joseph Maxwell
- Re: AMBER: mfef90 - installation problem Michael Crowley
- Re: AMBER: mfef90 - installation problem Joseph Maxwell
- AMBER: leap/frcmod problem Joseph Nachman
- Re: AMBER: leap/frcmod problem David A. Case
- Re: AMBER: Compiling sander with single precision Mengjuei Hsieh
- AMBER: Scyld cluster amber 7 compile problems Bengt Svensson
- AMBER: Amber 7 - bugfix 42 problem. Bengt Svensson
- AMBER: Suggestion regarding long simulation. uddhavesh bhaskar sonavane
Thursday, 18 September 2003
- AMBER: Calculating solvation energies for MM-PBSA use Thomas Steinbrecher
- Re: AMBER: Calculating solvation energies for MM-PBSA use samantha hughes
- AMBER: FEP problem Itziar Maestre Asenjo
- Re: AMBER: FEP problem David A. Case
- AMBER: re: MD problem!! Pradipta Bandyopadhyay
- Re: AMBER: Scyld cluster amber 7 compile problems Scott Brozell
- AMBER: Generalized Born parameters Peter VARNAI
- RE: AMBER: re: MD problem!! Yong Duan
- AMBER: MD problem!! Pradipta Bandyopadhyay
- Re: AMBER: MD problem!! yduan.udel.edu
- Re: AMBER: Suggestion regarding long simulation. Johannes Zuegg
- RE: AMBER: Suggestion regarding long simulation. Yong Duan
- Re: AMBER: Suggestion regarding long simulation. Carlos Simmerling
Friday, 19 September 2003
- Re: AMBER: Suggestion regarding long simulation. Carlos Simmerling
- AMBER: no defined type for atom N atom Wu Yingliang
- AMBER: no defined type for atom N atom Wu Yingliang
- Re: AMBER: no defined type for atom N atom David A. Case
- Re: AMBER: Amber 7 - bugfix 42 problem. David A. Case
- AMBER: xLEAP Problem Stephen P. Molnar, Ph.D.
- AMBER: 'high' temp. simulation!! Pradipta Bandyopadhyay
- AMBER: double bonds in prmtop Herbert Georg
- Re: AMBER: double bonds in prmtop Ioana Cozmuta
- RE: AMBER: xLEAP Problem Niko Jukarainen
- Re: AMBER: double bonds in prmtop Herbert Georg
- Re: AMBER: double bonds in prmtop David A. Case
- AMBER: C-alpha RMS Do Anh Tuan
Saturday, 20 September 2003
- AMBER: AMBER Carnal files Frederico.Miranda.ibmb.uib.no
- RE: AMBER: AMBER Carnal files Yong Duan
Sunday, 21 September 2003
- RE: AMBER: AMBER Carnal files Frederico.Miranda.ibmb.uib.no
- RE: AMBER: AMBER Carnal files Yong Duan
- Re: AMBER: xLEAP Problem Kazuo Koyano
- Re: AMBER: xLEAP Problem Donald Thomas
- AMBER: slow simulation nie beining
Monday, 22 September 2003
- Re: AMBER: C-alpha RMS Kun Song
- Re: AMBER: slow simulation David A. Case
- AMBER: plane angle. Pascal Bonnet
- AMBER: slower simulation nie beining
- Re: AMBER: slower simulation Carlos Simmerling
- AMBER: Antechamber problem Shafinaz
- AMBER: Slower simulation and pair-range cutoff? nie beining
- Re: AMBER: plane angle. Bill Ross
- AMBER: increase size of NATOM or NRES for "ambpdb" Wen Li
- Re: AMBER: increase size of NATOM or NRES for "ambpdb" David A. Case
- AMBER: Re: xLEAP Problem Stephen P. Molnar, Ph.D.
- AMBER: Carnal Input file Frederico.Miranda.ibmb.uib.no
- Re: AMBER: Carnal Input file Bill Ross
- RE: AMBER: Carnal Input file Ming Lei
Tuesday, 23 September 2003
- Re: AMBER: Antechamber problem David A. Case
- AMBER: How can I set ntx=7, but exclude the velocity? Margaret S. Cheung
- Re: AMBER: How can I set ntx=7, but exclude the velocity? Carlos Simmerling
- AMBER: pair-cutoff nie beining
- Re: AMBER: pair-cutoff David A. Case
Wednesday, 24 September 2003
- AMBER: mm_pbsa - ?small bugs? Chris Moth
Tuesday, 23 September 2003
- AMBER: GROUP Atchara Wijitkosoom
Wednesday, 24 September 2003
- AMBER: ?small bugs? - 2nd suggestion Chris Moth
Tuesday, 23 September 2003
- AMBER: residues and molecules GUILLERMINA L ESTIU
- AMBER: PMEMD 3.03 Update available Robert Duke
Wednesday, 24 September 2003
- AMBER: cd-c-os and c3-cd-c angle parameters Vikas Varshney
- Re: AMBER: cd-c-os and c3-cd-c angle parameters Junmei Wang
- Re: AMBER: residues and molecules David A. Case
- AMBER: problem with file format Shafinaz
- Re: AMBER: problem with file format David A. Case
- Re: AMBER: residues and molecules Robert Duke
- AMBER: NaCl ion pairs in TIP3P water box Nathan A. Baker
- RE: AMBER: problem with file format Shafinaz
- RE: AMBER: problem with file format Junmei Wang
- Re: AMBER: NaCl ion pairs in TIP3P water box Bill Ross
- Re: AMBER: NaCl ion pairs in TIP3P water box David A. Case
- Re: AMBER: NaCl ion pairs in TIP3P water box Jiri Sponer
- Re: AMBER: NaCl ion pairs in TIP3P water box Bill Ross
- Re: AMBER: NaCl ion pairs in TIP3P water box Ioana Cozmuta
- Re: AMBER: NaCl ion pairs in TIP3P water box M. L. Dodson
- Re: AMBER: NaCl ion pairs in TIP3P water box Nathan A. Baker
Thursday, 25 September 2003
- AMBER: MM_PBSA(GBSA) Examples Kazuo Koyano
- Re: AMBER: NaCl ion pairs in TIP3P water box Jiri Sponer
- Re: AMBER: NaCl ion pairs in TIP3P water box Pascal Auffinger
- AMBER: MM_PBSA(GBSA) Examples Chris Moth
- AMBER: Online model of 2C9 Peter Gannett
- AMBER: MeCNBOX northrop.chem.ucla.edu
- Re: AMBER: MeCNBOX David A. Case
- Re: AMBER: MeCNBOX northrop.chem.ucla.edu
- Re: AMBER: MeCNBOX northrop.chem.ucla.edu
- Re: AMBER: MeCNBOX James W. Caldwell
- AMBER: Re:MeCNBOX Pradipta Bandyopadhyay
Friday, 26 September 2003
- AMBER: about the mopac7 installation. Yong Wang
- Re: AMBER: MeCNBOX Pascal Bonnet
- Re: AMBER: MM_PBSA(GBSA) Examples Kazuo Koyano
- AMBER: Zn in antechamber Lishan Yao
- Re: AMBER: Zn in antechamber Junmei Wang
- Re: AMBER: Zn in antechamber Lishan Yao
- AMBER: non-bonded cutoffs Michael Dolan
- Re: AMBER: non-bonded cutoffs David A. Case
- Re: AMBER: non-bonded cutoffs Michael Dolan
- AMBER: Phase for torsion angle different of 0 or 180 ? Teletchéa Stéphane
- Re: AMBER: Zn in antechamber Junmei Wang
- Re: AMBER: Zn in antechamber Rhonda Torres
- Re: AMBER: Zn in antechamber Lishan Yao
- AMBER: FW: Residual dipolar couplings McAteer, Kathleen
- Re: AMBER: Zn in antechamber Junmei Wang
- Re: AMBER: FW: Residual dipolar couplings David A. Case
- Re: AMBER: Phase for torsion angle different of 0 or 180 ? David A. Case
Saturday, 27 September 2003
- AMBER: polarizability and PME Martin Mucha
- Re: AMBER: polarizability and PME David A. Case
Monday, 29 September 2003
- Re: AMBER: Zn in antechamber Lishan Yao
- Re: AMBER: Zn in antechamber Junmei Wang
- Re: AMBER: Zn in antechamber Lishan Yao
- Re: AMBER: Zn in antechamber Junmei Wang
- AMBER: AMBER quasih question(s) Rachel Ward
- Re: AMBER: Zn in antechamber Lishan Yao
- AMBER: nstlim Amber Administration
- Re: AMBER: nstlim Robert Duke
- AMBER: A problem about xleap Jiang Pengju
- AMBER: density equilibrium & harmonic restrain yuann
- AMBER: iam a newbie !!! Karthikeyan Pasupathy
- AMBER: following salt and waterbridges during a simulation Karsten Suhre
- AMBER: TTF parameters northrop.chem.ucla.edu
Tuesday, 30 September 2003
- Re: AMBER: iam a newbie !!! Vlad Cojocaru
- Re: AMBER: A problem about xleap John Bushnell
- Re: AMBER: improper Bill Ross
- AMBER: improper Li Ying

Last message date: Tue Sep 30 2003 - 21:53:01 PDT
Archived on: Mon Feb 03 2025 - 05:53:16 PST

Amber Archive Sep 2003 by date