Amber Archive Oct 2002: by date

Tuesday, 1 October 2002
- Re: write problem on IBM-AIX Nicolas Grima
- Re: NON-BONDED INTERACTION David A. Case
- Re: Is H-bonding really there? Ioana Cozmuta
- Questions on crosslinking residues Nicholson, James D Mr ARO
- antechamber web page Ioana Cozmuta
- Re: antechamber web page David A. Case
- tutorial on plastocyanin Ioana Cozmuta
Wednesday, 2 October 2002
- restart without velocities Michal Otyepka
- Re: restart without velocities Sanjeev B.S.
- Re: tutorial on plastocyanin David A. Case
- RE: Sander multiprocessors running problem with MPI Ross Walker
- Sander multiprocessors running problem with MPI William Wei
- xleap XENVIRONMENT Mark C. Ballew
- Re: Questions on crosslinking residues David A. Case
- Re: xleap XENVIRONMENT David A. Case
- RE: Questions on crosslinking residues Nicholson, James D Mr ARO
- RESP gaussian job crashing Nicholson, James D Mr ARO
Thursday, 3 October 2002
- Re: xleap XENVIRONMENT Lepsa
- regarding resp-doubts thenmalar rathinavelan
- about AMBER parallel edition Shimono Fumihiro
- atomicfluct Bimo Ario Tejo
- Re: about AMBER parallel edition Shimono Fumihiro
- Re: Questions on crosslinking residues M. L. Dodson
- Re: RESP gaussian job crashing James W. Caldwell
- Re: Questions on crosslinking residues David A. Case
- Re: regarding resp-doubts Wiktor Jurkowski
- Re: regarding resp-doubts Miguel de Federico
- Re: regarding resp-doubts David A. Case
- Re: regarding resp-doubts James W. Caldwell
- MM-GBSA and counterions Michael Ford
- Re: MM-GBSA and counterions David A. Case
- EGB = NaNQ Pratul Agarwal
- Re: xleap XENVIRONMENT Mark C. Ballew
- RE: RESP gaussian job crashing Nicholson, James D Mr ARO
- Re: RESP gaussian job crashing Carlos P. Sosa
- compiling SGI/mpi Ioana Cozmuta
- RE:SAMUEL METU sam_008_at_www.com
- RE:SAMUEL METU sam_008_at_www.com
- Re: compiling SGI/mpi David A. Case
- Re: compiling SGI/mpi Ioana Cozmuta
Friday, 4 October 2002
- RMSD calculation question Soonmin Jang
- Re: RESP gaussian job crashing David Smith
- Re: About the Memory allocation in MM_PBSA and SANDER Alan Leo
- Different numbers on different architectures. David Smith
- Re: compiling SGI/mpi David A. Case
- NTX / IREST inconsistency Bimo Ario Tejo
- Re: EGB = NaNQ Andreas Svrcek-Seiler
- Re: NTX / IREST inconsistency David A. Case
- Re: Different numbers on different architectures. David A. Case
- Re: EGB = NaNQ Pratul Agarwal
- (no subject) Ioana Cozmuta
Monday, 7 October 2002
- what are "end group interactions"? C. Klein
- How to generate PNA structure? A. Hungie
- xleap on a SGI Fuel Giulio Rastelli
- MACHINE file for Tru64 ES45 CUI, Guanglei
- geometry optimization/turning off Elec and Vdw terms Tom Bishop
- Re: geometry optimization/turning off Elec and Vdw terms Margaret Cheung
- AMBER6 on cluster Mako Furukawa
- Re: AMBER6 on cluster Mako Furukawa
- Re: xleap on a SGI Fuel David A. Case
Tuesday, 8 October 2002
- 2D RMSd Luo Liu
- Re: MACHINE file for Tru64 ES45 Chuck Schneider
- Re: MACHINE file for Tru64 ES45 CUI, Guanglei
- do I need to mutate H1 atoms to HC in a "not really" perturbed part of a molecule ? hagop demirdjian
- crdgrow Ioana Cozmuta
- Re: crdgrow Sanjeev B.S.
- rdparm Ioana Cozmuta
- (no subject) kbyun_at_wesleyan.edu
- LINMIN FAILURE hung_at_atc.atccu.chula.ac.th
- Re: crdgrow David A. Case
- Re: LINMIN FAILURE David A. Case
- Re: rdparm Elsa de Sousa Henriques
Wednesday, 9 October 2002
- Re: reaction field energy of a ligand in MM-PBSA Lepsa
- Re: SHAKE problem Pratul Agarwal
- nmr and positional restraint in input Peter Varnai
- reaction field energy of a ligand in MM-PBSA Giulio Rastelli
Thursday, 10 October 2002
- about dummy parameter of multiplicity sxzheng
- Re: nmr and positional restraint in input Christoph Brockmann
- MM-PBSA tutorial Giulio Rastelli
- trouble with snapshots GC option of MM_PBSA Michael Ford
- Re: trouble with snapshots GC option of MM_PBSA Michael Ford
- Re: trouble with snapshots GC option of MM_PBSA - Now no output for lig and rec Michael Ford
- solved: nmr and positional restraint in input Peter Varnai
- [Fwd: Re: trouble with snapshots GC option of MM_PBSA] Holger Gohlke
- IBELLY and NMROPT in sander Tom Bishop
- Dielectric constant for interior of proteins Pratul Agarwal
- Re: Dielectric constant for interior of proteins David A. Case
- Re: about dummy parameter of multiplicity David A. Case
- Re: MM-PBSA tutorial Holger Gohlke
- Re: Dielectric constant for interior of proteins Pratul Agarwal
- How to do 2dRMS in ptraj Ying Zhao
- question about antibodies Ioana Cozmuta
- Some error message on Leap Sichun Yang
- Re: Some error message on Leap Michael Ford
- Re: Some error message on Leap Ioana Cozmuta
- docking in amber? Sichun Yang
- problem in sander Ioana Cozmuta
Friday, 11 October 2002
- Re: problem in sander David A. Case
- volume of ucell too big!! sxzheng
- period boundary Shunzhou Wan
- DNA Tutorial: min_ntr.in Joel Konkle-Parker
Sunday, 13 October 2002
- perturbation of gln to glu M. L. Dodson
Monday, 14 October 2002
- Re: MM-PBSA tutorial Lepsa
- MM-PBSA and Insight's version of Delphi Emma.Sigfridsson_at_astrazeneca.com
- pressure variation coupled with taup value Vlad Cojocaru
- loss of disulfide bonds Nicolas Le Novere
- Re: loss of disulfide bonds Holger Gohlke
- Re: loss of disulfide bonds David A. Case
- Re: loss of disulfide bonds Natasja Brooijmans
- Re: loss of disulfide bonds Carlos Simmerling
- Re: loss of disulfide bonds James W. Caldwell
- Re: loss of disulfide bonds Richard Henchman
- CH2Cl2 box Eric ARNOULT
- Re: loss of disulfide bonds David A. Case
- Potential bug in gbsa.h of sander-7 Vlad
- Compiler & Hardware requirement of AMBER7 ? yuann
- Re: Compiler & Hardware requirement of AMBER7 ? David Case
Tuesday, 15 October 2002
- Computational alchemy Aldo Jongejan
- new telescopes-Maksutov-Cassegrain, reflector, refractor wang lan
- new telescopes-Maksutov-Cassegrain, reflector, refractor wang lan
- Dummy torsions Aldo Jongejan
- Error in Antechamber program in ammber7 Narang Manpreet Kaur
- Re: Error in Antechamber program in ammber7 Lepsa
- Re: Dummy torsions David A. Case
- Re: Error in Antechamber program in ammber7 David A. Case
- Bug in reading binary restart file with BOX parameters Vlad
- Re: Error in Antechamber program in ammber7 Narang Manpreet Kaur
Wednesday, 16 October 2002
- dummy parameters Pierre Mignon
- How to specify the counterion positions using xleap? A.Madhumalar
- Re: Error in Antechamber program in ammber7 David A. Case
- Re: How to specify the counterion positions using xleap? David A. Case
- Can I use belly and ntr at the same time? sxzheng
- Re: Bug in reading binary restart file with BOX parameters David A. Case
- Re: How to specify the counterion positions using xleap? James W. Caldwell
- Re: Can I use belly and ntr at the same time? David A. Case
- Molecular Dynamic procedure... Andrei Leit�o
- How to convert oldparmtop to newparmtop? A.Madhumalar
- error message Vlad Cojocaru
- more information about the previous email Vlad Cojocaru
- Re: error message Holger Gohlke
- Re: How to specify the counterion positions using xleap? Ioana Cozmuta
- Re: error message Natasja Brooijmans
- restraining atoms Ioana Cozmuta
- Re: error message Margaret Cheung
- Re: error message Andreas Svrcek-Seiler
- Re: How to convert oldparmtop to newparmtop? David A. Case
- IGB =4 with GAFF and bugfix24 incomplete? Tom Bishop
- syntax Ioana Cozmuta
- Re: confusing error messages David A. Case
- Re: IGB =4 with GAFF and bugfix24 incomplete? David A. Case
- Re: syntax David A. Case
- Re: error message Bill Ross
- Re: How to convert oldparmtop to newparmtop? Michael Ford
- Re: How to specify the counterion positions using xleap? M. L. Dodson
- Re: restraining atoms Lepsa
Thursday, 17 October 2002
- Sir, Venkanna Belde
- Imaging & fitting in carnal Sanjeev B.S.
- Truncated Octahedron Box giudice
- a leap question Vlad Cojocaru
- Re: a leap question CUI, Guanglei
- Re: a leap question David A. Case
- dummy torsional parameters again. X. Tan
- Re: How to convert oldparmtop to newparmtop? A.Madhumalar
- sander6 running and crashing at PSC? CUI, Guanglei
- Re: restraining atoms Ioana Cozmuta
- Re: dummy torsional parameters again. David A. Case
- Solvent exposed surface area over a trajectory Rebecca Perlow
- Re: Solvent exposed surface area over a trajectory Michael Ford
- Re: Solvent exposed surface area over a trajectory Sanjeev B.S.
- Reference for GB model 2 Jianhui Wu
- Sander segmentation fault Joel Konkle-Parker
- Reference, GB 2, Amber7 Jianhui Wu
- Re: Solvent exposed surface area over a trajectory Natasja Brooijmans
- time averaged restraint parameters Jake Isaacs
- Re: Reference for GB model 2 Andreas Svrcek-Seiler
- cutoffs in GB David A. Case
Friday, 18 October 2002
- Carnal table output Christoph Brockmann
- targeted MD Giulio Rastelli
- Re: Carnal table output Holger Gohlke
- Re: targeted MD David A. Case
- Re: targeted MD Carlos Simmerling
- Not able to use xleap ... St�phane Teletch�a
- Re: Not able to use xleap ... CUI, Guanglei
- Re: Not able to use xleap ... David A. Case
- Re: Not able to use xleap ... CUI, Guanglei
- Re: Not able to use xleap ... St�phane Teletch�a
- allocation memory error Ioana Cozmuta
- Amber 4 question Tod Pascal
Saturday, 19 October 2002
- RE: Not able to use xleap ... Ross Walker
- Re: targeted MD Peter VARNAI
- number of H-bonds Bimo Ario Tejo
- Re: number of H-bonds Sanjeev B.S.
Sunday, 20 October 2002
- How to define a sphere to minimize? Guillermo Mulliert Carl�n
Monday, 21 October 2002
- Re: Not able to use xleap ... St�phane Teletch�a
- Re: How to define a sphere to minimize? David Smith
- Re: Not able to use xleap ... CUI, Guanglei
- Re: Not able to use xleap ... St�phane Teletch�a
- Re: How to define a sphere to minimize? Bill Ross
- Re: Not able to use xleap ... CUI, Guanglei
- Re: reg: MAC OS David A. Case
- Re: reg: MAC OS Mengjuei Hsieh
- question on ouput of sander Sichun Yang
- Re: question on ouput of sander CUI, Guanglei
- Re: question on ouput of sander Sichun Yang
- Re: question on ouput of sander David A. Case
- sander7: MPI_COMM_RANK problem Matteo Dal Peraro
- scaling of amber with number of atoms Marcela Madrid
- systems.Re: sander7: MPI_COMM_RANK problem Carlos P. Sosa
- problem with gibbs !!!! Asif Rahaman
Tuesday, 22 October 2002
- MM-PGBSA Question!! Bernd Wellenzohn
- Re: Compiler & Hardware requirement of AMBER7 ? yuann
- Re: problem with gibbs !!!! James W. Caldwell
- Re: MM-PGBSA Question!! David A. Case
- Amber Crd format Tod Pascal
- Re: Amber Crd format Natasja Brooijmans
- mm_pbsa-amber7 Sue Heavner
- replacing fft routines Florian Barth
- Re: allocation memory error Ioana Cozmuta
- Re: replacing fft routines David A. Case
Wednesday, 23 October 2002
- Dummy atoms... Miguel de Federico
- Re: Patching AMBER7 with #24 Lepsa
- Re: Patching AMBER7 with #24 Lepsa
- Re: Dummy atoms... David A. Case
- Amber6 and MPI Yu Chen
- Antechamber generating bad charges w/ gaussian 98. Nicholson, James D Mr ARO
- Re: Antechamber generating bad charges w/ gaussian 98. James W. Caldwell
- min output Ioana Cozmuta
- Re: min output David A. Case
- RE: Antechamber generating bad charges w/ gaussian 98. Nicholson, James D Mr ARO
- RE: Antechamber generating bad charges w/ gaussian 98. Nicholson, James D Mr ARO
Thursday, 24 October 2002
- SDS forcefield? Arvid Soederhaell
- Protein jump out, please help Lich Nguyen
- Re: min output James W. Caldwell
- Re: Protein jump out, please help Michael G Cooney
- carnal output trajectory Vlad Cojocaru
- Re: carnal output trajectory Margaret Cheung
- residue cross-correlation Bimo Ario Tejo
- Re: carnal output trajectory Bill Ross
- Re: HIS residues Ioana Cozmuta
- Re: HIS residues Natasja Brooijmans
- Re: Protein jump out, please help Lich Nguyen
Friday, 25 October 2002
- carnal output trajectory Vlad Cojocaru
- Re:SURFTEN for GB Lepsa
- Fw: Re:SURFTEN for GB Lepsa
- once again: residue cross-correlation Bimo Ario Tejo
- time correlation function Bimo Ario Tejo
- specification for memory requirement yuann
- Re: specification for memory requirement Carlos Simmerling
Sunday, 27 October 2002
- 2nd restart CUI, Guanglei
- total energies during MM-PBSA Giulio Rastelli
- Amber vijay dasa
Monday, 28 October 2002
- Hello Amber, vijay dasa
- leap - sander information flow Wiktor Jurkowski
- Targeted MD Giulio Rastelli
- Re: leap - sander information flow David A. Case
- quasih Pratul Agarwal
- Re: Targeted MD Carlos Simmerling
- 64-bit Compilation SUN's forte compiler Fernando Martin
- Re: 64-bit Compilation SUN's forte compiler Ioana Cozmuta
- Re: 64-bit Compilation SUN's forte compiler Scott Brozell
- RE: 64-bit Compilation SUN's forte compiler Fernando Martin
- Re: 64-bit Compilation SUN's forte compiler David A. Case
Tuesday, 29 October 2002
- LEaP: The parm and coord files disagree on the number of atoms Miguel de Federico
- FEP - ligand to nothing (or water)?? Aldo Jongejan
- Re: FEP - ligand to nothing (or water)?? David A. Case
- Re: LEaP: The parm and coord files disagree on the number of atoms James W. Caldwell
- mm_pbsa curious output of coordinates and resulting errors... Michael Ford
- mm_pbsa error message (warning?) Michael Ford
- Problems with tes.antechamber Chen, Ya
Wednesday, 30 October 2002
- Resp Multiconformational charge fitting! Marco Aur�lio Correia Preto
- carnal output trajectory Vlad Cojocaru
- Re: carnal output trajectory St�phane Teletch�a
- Re: carnal output trajectory Sanjeev B.S.
- Sander Recompilation for the Biotin-Streptavidin Tutorial? Thomas Steinbrecher
- Re: carnal output trajectory Bill Ross
- Charges derivation question! Marco Aur�lio Correia Preto
- Re: RESP-group constraint Marco Preto
- IDECOMP Mark Hsieh
- Re: IDECOMP Holger Gohlke
- question on belly and restraint Sichun Yang
- How to choose the box and cap size sxzheng
Thursday, 31 October 2002
- Re: time correlation function David A. Case
- *.top file: "PARM-F-UHOSED, try again" david
- Re: *.top file: "PARM-F-UHOSED, try again" David A. Case
- Re: *.top file: "PARM-F-UHOSED, try again" Michael Ford
- carnal Ioana Cozmuta
- xleap and modified sugar residues Michael Ford
- Re: xleap and modified sugar residues Holger Gohlke
- NAV detected a virus in a document YOU sent to webmaster.nctimes.com. Mercury
Wednesday, 30 October 2002
- MD steps limit in sander (Amber 6) Marco Preto
- Re: MD steps limit in sander (Amber 6) Marco Preto
- Re: no MD output Marco Preto
- Minimization problem w/ counter-ion ! Marco Preto
- Re: Minimization problem w/ counter-ion ! Marco Preto
- NVT system implosion!!! Marco Preto
- Re: NVT system implosion!!! Marco Preto

Last message date: Thu May 29 2003 - 09:53:00 PDT
Archived on: Wed Dec 25 2024 - 05:53:19 PST

Amber Archive Oct 2002 by date