Amber Archive Apr 2003: by date

Tuesday, 1 April 2003
- Examples for Energy Minimisation methods S.Swaminathan
- Polarizable simulation2 Lepsa
- Problem of Hbond in CARNAL yuann
- Re: Problem of Hbond in CARNAL sychen
- size of a simulation system Wen Li
- Re: Examples for Energy Minimisation methods Carlos P. Sosa
- Re: AMBER pdb help - lost atoms David A. Case
- AMBER pdb help - lost atoms kxg2248.njit.edu
- Re: size of a simulation system David A. Case
- Re: Polarizable simulation2 David A. Case
- Re: AMBER pdb help - lost atoms Ioana Cozmuta
- RE: size of a simulation system Kristina Furse
- Re: AMBER pdb help - lost atoms David A. Case
- A weird antechamber error Yuhui Cheng
- About electrostatic force calculations Soonmin Jang
Wednesday, 2 April 2003
- old prmtop format in AMBER 6 differs from what is presented in AMBER 7 manual Filip Ryj�cek
- Re: size of a simulation system Pratul Agarwal
- Re: A weird antechamber error David A. Case
- Re: size of a simulation system Ioana Cozmuta
- Using MPI, PBS Venkata S Koppuravuri
- Re: Using MPI, PBS Ioana Cozmuta
- Re: Using MPI, PBS Carlos Simmerling
- (no subject) dicksmit.umich.edu
- Re: size of a simulation system Pratul Agarwal
- Beyond 1,000,000 atoms Vlad
Thursday, 3 April 2003
- Side-chain/main-chain decomposition in MM-GBSA Lepsa
- Hydrogen bond energy Dr.K.Veluraja
- Unit of velocity A. Hungie
- Re: Unit of velocity David A. Case
- Re: AMBER pdb help - lost atoms - Part 2 David A. Case
- Re: Hydrogen bond energy David A. Case
- Re: Unit of velocity A. Hungie
- Re: AMBER pdb help - lost atoms - Part 2 kxg2248.njit.edu
- New Machine.sgi_mpi file Roberto Gomperts
- frcmod file Wen Li
- anal question Hai-Long Wang
- Re: Side-chain/main-chain decomposition in MM-GBSA Holger Gohlke
Friday, 4 April 2003
- general minimisation methods S.Swaminathan
- ptraj problem Sophia Kondratova
- frcmod file for Free energy perturbation tutorial of valine to alanine dicksmit.umich.edu
- free energy calculations Joseph Fernandez
Sunday, 6 April 2003
- Re: sander & prmtop file generated from antechamber input ? sychen
- Re: sander & prmtop file generated from antechamber input ? David A. Case
Monday, 7 April 2003
- please kindly help S.Swaminathan
- (no subject) Carolina Salvador-Morales
- Re: please kindly help David A. Case
- growing side chains Robert G. Endres
- Nitro group introduction in tyrosine residue chandran karunakaran
- a-Helix direction? William Wei
- Trouble with AMBER 7 Shafinaz
Tuesday, 8 April 2003
- protonate S.Swaminathan
- problem with tleap S.Swaminathan
- addles Samy Name_removed_after_user_request
- very important Shafinaz
- Re: very important CUI, Guanglei
- mm_pbsa & nmode FyD
- Re: protonate David A. Case
- mutating residues Craig A Bayse
- Re: problem with tleap David A. Case
- The error in the trajectory file Ling Zhang
- question about MM-PBSA? Lishan Yao
- characteristics of nucleic acids homopolymers Ioana Cozmuta
- Groups defenition Javier Cuervo
- Periodic Boundary Condition in AMBER7 (the sander module)! Dat H. Nguyen
- Re: Periodic Boundary Condition in AMBER7 (the sander module)! David A. Case
- Tleap chandran karunakaran
- nmode for S calculation wentaofu
- Trying to understand parm99.dat Sichun Yang
- Re: Tleap David A. Case
- RE: Trying to understand parm99.dat Yong Duan
Wednesday, 9 April 2003
- Re: Groups defenition David A. Case
Thursday, 10 April 2003
- SANDER Source Code Documentation Jones, Garth A
- Amber7 and mpirun on Linux Wen Li
- Re: Amber7 and mpirun on Linux Scott Brozell
- free energy in sander Joseph Fernandez
- Re: free energy in sander David A. Case
- Re: Tleap-metalloprotein chandran karunakaran
- RE: Tleap-metalloprotein Yong Duan
- Re: free energy in sander Joseph Fernandez
Friday, 11 April 2003
- Usubscribe Miguel de Federico
- RE: Amber7 and mpirun on Linux Francesc Corcho
- Bugfixes Francesc Corcho
- Re: Bugfixes Natasja Brooijmans
- RE: Amber7 and mpirun on Linux Scott Brozell
- SSBonds and charge problems Steve Seibold
- Re: SSBonds and charge problems caldwell.heimdal.compchem.ucsf.edu
- Re: SSBonds and charge problems David A. Case
Saturday, 12 April 2003
- Amber on Linux Wen Li
- Re: Amber on Linux Viktor Hornak
Sunday, 13 April 2003
- Re: Amber on Linux Wen Li
- ALA-scan problem with mm_pbsa.pl Natasja Brooijmans
- diffusion coefficients yuan bo
- RE: diffusion coefficients Yong Duan
- Re: diffusion coefficients David A. Case
Monday, 14 April 2003
- To: amber as a Nicer Person Dr. Carter, President
- A problem in Sander production dynamics yuann
- Re: A problem in Sander production dynamics Carlos Simmerling
- Re: addles Carlos Simmerling
- Re: A problem in Sander production dynamics Thomas Cheatham
- Re: diffusion coefficients Thomas Cheatham
- id_torus(): Could not find torus for atoms 1878 and 1894 Yunfeng Hu
- Metalloprotein chandran karunakaran
- A problem in opening the file Khanh.Dao.iac.uib.no
- Re: A problem in opening the file David A. Case
Tuesday, 15 April 2003
- Re: A problem in opening the file Khanh.Dao.iac.uib.no
- PME box information Khanh.Dao.iac.uib.no
- solvents aren't loading Mac Brown
- Proper Restraint usage Steve Seibold
- Re: Proper Restraint usage David A. Case
- Re: Proper Restraint usage CUI, Guanglei
- ibelly and ntr Youyi Peng
- Re: ibelly and ntr David A. Case
- AMBER chandran karunakaran
- Re: AMBER CUI, Guanglei
- Re: AMBER David A. Case
- ambpdb Youyi Peng
- Re: AMBER chandran karunakaran
- No statistical output for MM-PBSA? Lishan Yao
- Re: ibelly and ntr sychen
- Re: ambpdb Luis Gracia
Wednesday, 16 April 2003
- Re: ambpdb Florian Barth
- CYS and HIS Youyi Peng
- Re: CYS and HIS caldwell.heimdal.compchem.ucsf.edu
- MPI run problem William Wei
- velocity auto-correlation function A. Hungie
- Re: ALA-scan problem with mm_pbsa.pl Holger Gohlke
- Re: No statistical output for MM-PBSA? Holger Gohlke
- Re: ALA-scan problem with mm_pbsa.pl Natasja Brooijmans
- RE: ibelly and ntr Kristina Furse
- Adding ACE to chopped protein Karl N. Kirschner
- Re: CCL:MPI run problem Carlos Simmerling
- makeDIST_RST Youyi Peng
Thursday, 17 April 2003
- ambpdb and protonate in AMBER7 Francisco Blanco
- Organic solvents Carlos P. Sosa
- quasih cailliez
- unsubscribe from the mail list Xiaoqin Huang
- Re: makeDIST_RST David A. Case
- question about MM-PBSA? Lishan Yao
- topology file in large systems GUILLERMINA L ESTIU
- Re: topology file in large systems caldwell.heimdal.compchem.ucsf.edu
- Re: question about MM-PBSA? Holger Gohlke
Friday, 18 April 2003
- Re: question about MM-PBSA? Lishan Yao
- MD went crazy Youyi Peng
- Re: MD went crazy Carlos Simmerling
- Re: MD went crazy Youyi Peng
- Re: ambpdb Venkata S Koppuravuri
- Re: MD went crazy Carlos Simmerling
- Re: MD went crazy Youyi Peng
- Re: MD went crazy Michael Crowley
- Re: MD went crazy Carlos Simmerling
- Re: MD went crazy Youyi Peng
- Re: MD went crazy Youyi Peng
- Re: MD went crazy Carlos Simmerling
- Re: MD went crazy Youyi Peng
- MM-GBSA question Javier Cuervo
Saturday, 19 April 2003
- debug leap vze6jslz.verizon.net
- Re: debug leap Scott Brozell
Sunday, 20 April 2003
- AMBER chandran karunakaran
Monday, 21 April 2003
- (no subject) Khanh.Dao.iac.uib.no
- trouble with OFF files Mac Brown
- Re: trouble with OFF files M. L. Dodson
- Problem Finishing Tutorial Derek Smith
- Re: Problem Finishing Tutorial Ioana Cozmuta
- Re: question about MM-PBSA? Lepsa
Tuesday, 22 April 2003
- Re: Fwd: Re: Request for Amber7 (fwd) Rajendra P. OJHA
- Organic Solvents Petrodler.aol.com
- Re: Organic Solvents Jose Ramon Blas
- How to use GLYCAM force field in AMBER Peng Tao
- mm_pbsa_statistics.pm kbyun.wesleyan.edu
- Re: Request for Amber7 (xleap problem) John Bushnell
Wednesday, 23 April 2003
- converting amber to gromos format Jake Isaacs
- GB/SA Robert G. Endres
- mm_pbsa nmode calculation kbyun.wesleyan.edu
- anyone have AMBER benchmarks with gigabit ethernet? Carlos Simmerling
- Re: mm_pbsa nmode calculation Holger Gohlke
- Re: GB/SA David A. Case
- Re: mm_pbsa nmode calculation kbyun.wesleyan.edu
- Re: How to use GLYCAM force field in AMBER David A. Case
- leap problem yuan bo
Thursday, 24 April 2003
- Problem_to_open_PROTON_INFO_file Khanh.Dao.iac.uib.no
- RE: anyone have AMBER benchmarks with gigabit ethernet? Ross Walker
- RE: anyone have AMBER benchmarks with gigabit ethernet? Ross Walker
- Re: Problem_to_open_PROTON_INFO_file David A. Case
- non bonded pair list Jean-François Taly
- Question: Nmode with counter ions. Masaki Tomimoto
- PSC Summer Workshop: Modeling from Protein Sequence to Structure Troy Wymore
- job stopped Youyi Peng
- Re: job stopped CUI, Guanglei
- Re: job stopped Youyi Peng
- Re: job stopped Natasja Brooijmans
- Future of structural biology conference David Cowburn
- Annealing blown up Nick Polfer
- Re: Problem_to_open_PROTON_INFO_file Venkata S Koppuravuri
- Re: job stopped Youyi Peng
- Re: job stopped CUI, Guanglei
- Re: Question: Nmode with counter ions. David A. Case
- Re: Annealing blown up David A. Case
- Re: non bonded pair list David A. Case
Friday, 25 April 2003
- question about H-bond in carnal? Lishan Yao
- Re: question about H-bond in carnal? Sanjeev B.S.
- Re: question about H-bond in carnal? Lishan Yao
- Re: question about H-bond in carnal? Sanjeev B.S.
- Re: question about H-bond in carnal? Bill Ross
- nmode and mm_pbsa questions? wentaofu
- Re: nmode and mm_pbsa questions? Holger Gohlke
Sunday, 27 April 2003
- Re: question about H-bond in carnal? Lishan Yao
Monday, 28 April 2003
- troubles on RS6000 Wayne Dawson
- Re: GB/SA Robert G. Endres
- how to restrain base pair Shuang Ding
- Re: how to restrain base pair David A. Case
- Amber on Parallel Sun? Bengt Svensson
- Protein - DNA complex simulation - protocol Harikrishnan
- problem_namelist_reading Khanh.Dao.iac.uib.no
- Re: question about H-bond in carnal? Sanjeev B.S.
- test Dr.Rajendra Joshi
Tuesday, 29 April 2003
- Re: Protein - DNA complex simulation - protocol Andreas Svrcek-Seiler
- any one has references to parallelization aspects of AMBER Satish Kumar
- Re: any one has references to parallelization aspects of AMBER Harikrishnan
- atom position restraints Yuuki Komata
- Re: Protein - DNA complex simulation - protocol Harikrishnan
- force field parameters for phosphoserine Christoph Kluck
- Re: Protein - DNA complex simulation - protocol Pratul Agarwal
- Re: force field parameters for phosphoserine David A. Case
- Re: problem_namelist_reading David A. Case
- Description of ATOM type in GLYCAM Peng Tao
- Future of Structural Biology Conference, 2003, http://futurestructuralbiology.org David Cowburn
- Re: Description of ATOM type in GLYCAM FyD
- phi and psi angles analysis Xiao Jian Tan
- Re: phi and psi angles analysis Holger Gohlke
- about molecular dynamics ronnie
- Re: about molecular dynamics Carlos Simmerling
- atom position restraints Yuuki Komata
- Re: phi and psi angles analysis Guanglei Cui
- Re: about molecular dynamics Carlos Simmerling
- Re: problem_namelist_reading Khanh.Dao.iac.uib.no
Wednesday, 30 April 2003
- Residual dipolar couplings McAteer, Kathleen
- Re: GB/SA Robert G. Endres
- carnal hbond Hai-Long Wang

Last message date: Fri May 02 2003 - 00:53:01 PDT
Archived on: Mon Nov 03 2025 - 05:53:21 PST

Amber Archive Apr 2003 by date