Amber Archive Jun 2010: by date

Monday, 31 May 2010
- Re: [AMBER] Is it possible to plot RMSd VS residue number for a protein? Homa Azizian
- Re: [AMBER] MMPBSA.py update install problem Rilei Yu
- [AMBER] Prepare the mutants file for ala scanning Rilei Yu
- [AMBER] Problem on B-factor Calculation tianyuan meng
- [AMBER] Why different binding energy is obtained from GBSA calculations? Catein Catherine
Tuesday, 1 June 2010
- [AMBER] discontinuous residues Jio M
- [AMBER] Polak Ribiere Jagdeesh C
- Re: [AMBER] Polak Ribiere Mengjuei Hsieh
- [AMBER] Error in estrogen-raloxifene tutorial vaibhav dixit
- [AMBER] MMPBSA problem binding energy calculation kamlesh sahu
- Re: [AMBER] Prepare the mutants file for ala scanning Gustavo Seabra
- Re: [AMBER] MMPBSA problem binding energy calculation Bill Miller III
- Re: [AMBER] amber10 installtion error in parallel Jason Swails
- Re: [AMBER] Error in estrogen-raloxifene tutorial Jason Swails
- Re: [AMBER] MMPBSA problem binding energy calculation Dwight McGee
- Re: [AMBER] discontinuous residues Jason Swails
- [AMBER] error: mask from topology files! vaibhav dixit
- Re: [AMBER] error: mask from topology files! Bill Miller III
- [AMBER] sleap log Omair A. Khan
- [AMBER] amber10 compilation Sangita Kachhap
- Re: [AMBER] reg REMD Dongshan Wei
- Re: [AMBER] Is it possible to plot RMSd VS residue number for a protein? M. Reza Ganjalikhany
- Re: [AMBER] reg REMD Daniel Roe
- Re: [AMBER] amber10 compilation Jason Swails
- Re: [AMBER] amber10 compilation Daniel Roe
- Re: [AMBER] Polak Ribiere Bill Ross
- Re: [AMBER] discontinuous residues Jio M
- [AMBER] AMBER10 TI calculations manikanthan bhavaraju
- Re: [AMBER] CUDA Segfault GTX470 Levi Pierce
- RE: [AMBER] CUDA Segfault GTX470 Ross Walker
- [AMBER] MM_PBSA: multiple processes, single point output along the trajecotry and cropped structures Yuqin Cai
- Re: [AMBER] CUDA Segfault GTX470 Levi Pierce
- Re: [AMBER] MM_PBSA: multiple processes, single point output along the trajecotry and cropped structures Dwight McGee
- Re: [AMBER] AMBER10 TI calculations case
- Re: [AMBER] MM_PBSA: multiple processes, single point output along the trajecotry and cropped structures Dwight McGee
- Re: [AMBER] MM_PBSA: multiple processes, single point output along the trajecotry and cropped structures Jason Swails
- Re: [AMBER] sleap log case
- [AMBER] pmemd.cuda - ewald error estimate? Paul Brandt
- RE: [AMBER] pmemd.cuda - ewald error estimate? Ross Walker
- Re: [AMBER] MMPBSA problem binding energy calculation kamlesh sahu
- Re: [AMBER] MMPBSA problem binding energy calculation Jason Swails
- Re: [AMBER] MMPBSA problem binding energy calculation kamlesh sahu
- Re: [AMBER] MMPBSA problem binding energy calculation Bill Miller III
- Re: [AMBER] MMPBSA problem binding energy calculation kamlesh sahu
- Re: [AMBER] MMPBSA problem binding energy calculation kamlesh sahu
- Re: [AMBER] MMPBSA problem binding energy calculation Bill Miller III
- Re: [AMBER] MMPBSA.py update install problem Rilei Yu
- [AMBER] The charge xuemeiwang1103
Wednesday, 2 June 2010
- Re: [AMBER] MMPBSA.py update install problem Dwight McGee
- Re: [AMBER] MMPBSA.py update install problem Rilei Yu
- [AMBER] Error: No potential terms in sander output! vaibhav dixit
- Re: [AMBER] MMPBSA.py update install problem Bill Miller III
- [AMBER] Re: Error: No potential terms in sander output! Bill Miller III
- Re: [AMBER] Re: Error: No potential terms in sander output! Jim Paugh
- Re: [AMBER] AmberTools-1.4 Test Problem Gustavo Seabra
- [AMBER] distance restraints qiaoyan
- Re: [AMBER] MMPBSA.py update install problem Jason Swails
- Fwd: Re: Re: [AMBER] error - binding_energy.mmpbsa run Andrew Voronkov
- Re: [AMBER] distance restraints Jason Swails
- Re: Re: Re: [AMBER] error - binding_energy.mmpbsa run Jason Swails
- Re: [AMBER] Parallel installation of AMBER 11 on MacOSX George Tzotzos
- Re: [AMBER] distance restraints Bill Ross
- Re: [AMBER] Parallel installation of AMBER 11 on MacOSX Jason Swails
- Re: [AMBER] Parallel installation of AMBER 11 on MacOSX George Tzotzos
- Re: [AMBER] Parallel installation of AMBER 11 on MacOSX Bill Ross
- Re: [AMBER] Parallel installation of AMBER 11 on MacOSX George Tzotzos
- Re: [AMBER] Parallel installation of AMBER 11 on MacOSX Jason Swails
- Re: [AMBER] Parallel installation of AMBER 11 on MacOSX Bill Ross
- Re: [AMBER] Parallel installation of AMBER 11 on MacOSX George Tzotzos
- Re: [AMBER] distance restraints Jason Swails
- [AMBER] restraint in umbrella sampling dhacademic
- Re: [AMBER] restraint in umbrella sampling Jason Swails
- [AMBER] Is it possible to revome water molecules during simulation? Hoshin Kim
- Re: [AMBER] Is it possible to revome water molecules during simulation? Bill Ross
- Re: [AMBER] Is it possible to revome water molecules during simulation? Jason Swails
- Re: [AMBER] The charge Ray Luo
Thursday, 3 June 2010
- RE: [AMBER] Is it possible to revome water molecules during simulation? Hoshin Kim
Wednesday, 2 June 2010
- RE: [AMBER] Is it possible to revome water molecules during simulation? Bill Ross
- Re: [AMBER] MMPBSA.py update install problem Rilei Yu
Thursday, 3 June 2010
- [AMBER] time-correlation fluctuation Homa Azizian
- Re: Re: Re: Re: [AMBER] error - binding_energy.mmpbsa runRe: Re: Re: Re: [AMBER] error - binding_energy.mmpbsa run Andrew Voronkov
- Re: Re: Re: Re: [AMBER] error - binding_energy.mmpbsa runRe: Re: Re: Re: [AMBER] error - binding_energy.mmpbsa run Bill Miller III
- RE: [AMBER] amber11 PMEMD cuda problem. (sometimes stopped...) Ross Walker
- [AMBER] mm_pbsa error on ambertools 1.4 amber11 ANDREA.MEZGEZ.dicamp.units.it
- Re: [AMBER] mm_pbsa error on ambertools 1.4 amber11 Jason Swails
- [AMBER] Lmod, NAB error Cristina Sisu
- Re: [AMBER] Lmod, NAB error Jason Swails
- Re: [AMBER] Lmod, NAB error Cristina Sisu
- Re: [AMBER] Lmod, NAB error Bill Ross
- Re: [AMBER] Lmod, NAB error Cristina Sisu
- [AMBER] ALASCAN (Alanine scanning mutagens ) Sushil Mishra
- Re: [AMBER] sleap log Omair A. Khan
- Re: [AMBER] sleap log case
- [AMBER] How to restart the remd simulation following the remd tutorial? Dongshan Wei
Friday, 4 June 2010
- [AMBER] cutoff fancy2012
- RE: [AMBER] mm_pbsa error on ambertools 1.4 amber11 ANDREA.MEZGEZ.dicamp.units.it
- [AMBER] About water molecule analysis gokul algates
- Re: [AMBER] How to restart the remd simulation following the remd tutorial? Daniel Roe
- [AMBER] tleap: C-N triple bond and sp1 hybridization vedat durmaz
- Re: [AMBER] tleap: C-N triple bond and sp1 hybridization case
- Re: [AMBER] mm_pbsa error on ambertools 1.4 amber11 Jason Swails
- Re: [AMBER] tleap: C-N triple bond and sp1 hybridization vedat durmaz
- Re: [AMBER] ALASCAN (Alanine scanning mutagens ) Dwight McGee
- Re: [AMBER] ALASCAN (Alanine scanning mutagens ) Sushil Mishra
- Re: [AMBER] ALASCAN (Alanine scanning mutagens ) Dwight McGee
- [AMBER] simulation of protein ashutosh shandilya
- [AMBER] simulation of protein ashutosh shandilya
- Re: [AMBER] tleap: C-N triple bond and sp1 hybridization case
- Re: [AMBER] tleap: C-N triple bond and sp1 hybridization Bill Ross
- Re: [AMBER] cutoff Bill Ross
- Re: [AMBER] simulation of protein Bill Ross
- Re: [AMBER] simulation of protein Gustavo Seabra
- Re: [AMBER] simulation of protein ashutosh shandilya
- [AMBER] Amber on BlueGene/P T. Andrew Binkowski
- Re: [AMBER] simulation of protein Bill Ross
- Re: [AMBER] simulation of protein ashutosh shandilya
- Re: [AMBER] simulation of protein ashutosh shandilya
- Re: [AMBER] simulation of protein Jason Swails
- Re: [AMBER] Amber on BlueGene/P case
- Re: [AMBER] simulation of protein Bill Ross
- [AMBER] entropy calculation failed again! Rilei Yu
- Re: [AMBER] entropy calculation failed again! Dwight McGee
- Re: [AMBER] entropy calculation failed again! Bill Miller III
- Re: [AMBER] entropy calculation failed again! Dwight McGee
- Re: [AMBER] entropy calculation failed again! Rilei Yu
- Re: [AMBER] entropy calculation failed again! Bill Miller III
- Re: [AMBER] entropy calculation failed again! Dwight McGee
- Re: [AMBER] entropy calculation failed again! Rilei Yu
- [AMBER] gb working but not pb & gives No potential terms in sander output! error vaibhav dixit
- [AMBER] MMPBSA.py calculations...bad atom type RANAJIT SHINDE
- [AMBER] MMPBSA.py calculations...bad atom type RANAJIT SHINDE
Saturday, 5 June 2010
- [AMBER] Re: gb working but not pb & gives No potential terms in sander output! error Bill Miller III
- Re: [AMBER] MMPBSA.py calculations...bad atom type Bill Miller III
- Re: [AMBER] entropy calculation failed again! case
- Re:Re: [AMBER] cutoff fancy2012
- [AMBER] Thr -> Met in TI calculation fancy2012
- Re: [AMBER] MMPBSA.py calculations...bad atom type Jason Swails
- Re: [AMBER] Thr -> Met in TI calculation Jason Swails
- RE: Re: [AMBER] cutoff Ross Walker
- [AMBER] Fourier terms Hector A. Baldoni
- Re:Re: [AMBER] cutoff Bill Ross
- RE: Re: [AMBER] cutoff Bill Ross
- Re: [AMBER] cutoff Dean Cuebas
- Re: [AMBER] cutoff Bill Ross
- [AMBER] Entropy for my system works now Rilei Yu
Sunday, 6 June 2010
- Re:RE: Re: [AMBER] cutoff fancy2012
- [AMBER] Re: gb working but not pb & gives No potential terms in sander output! error vaibhav dixit
- [AMBER] Re: gb working but not pb & gives No potential terms in sander output! error Bill Miller III
- [AMBER] Entropy calculation using nmode in mm_pbsa.pl Sushil Mishra
- RE: [AMBER] cutoff Ross Walker
- Re: [AMBER] cutoff Dean Cuebas
- Re: [AMBER] MMPBSA.py calculations...bad atom type RANAJIT SHINDE
- [AMBER] The err of sander.PUPIL Aurum Bai
- [AMBER] Re: gb working but not pb & gives No potential terms in sander output! error vaibhav dixit
- Re: [AMBER] The err of sander.PUPIL Jason Swails
- [AMBER] #RECMAP + #LIGMAP != #COMPRI in .DECOMP of mm_pbsa.pl Sushil Mishra
Monday, 7 June 2010
- [AMBER] Error installing AMBER 10 on ubuntu Catein Catherine
- RE: [AMBER] Error installing AMBER 10 on ubuntu Catein Catherine
- Re: [AMBER] The err of sander.PUPIL Aurum Bai
- [AMBER] about ewald error estimate Navanath Kumbhar
- [AMBER] Amber11: running ptraj George Tzotzos
- [AMBER] Re: #RECMAP + #LIGMAP != #COMPRI in .DECOMP of mm_pbsa.pl Sushil Mishra
- Re: [AMBER] Amber11: running ptraj case
- Re: [AMBER] about ewald error estimate case
- Re: [AMBER] Error installing AMBER 10 on ubuntu case
- [AMBER] AMBER11 compilation Steve Seibold
- Re: [AMBER] AMBER11 compilation case
- RE: [AMBER] AMBER11 compilation Steve Seibold
- RE: [AMBER] Error installing AMBER 10 on ubuntu Catein Catherine
- Re: [AMBER] AMBER11 compilation case
- Re: [AMBER] Error installing AMBER 10 on ubuntu case
- [AMBER] Fwd: FW: Requesting your help in amber Jenny Iskrenova
- [AMBER] amber.cuda performance on Nvidia S2050? Sasha Buzko
- RE: [AMBER] amber.cuda performance on Nvidia S2050? Scott Le Grand
- Re: [AMBER] amber.cuda performance on Nvidia S2050? Sasha Buzko
- Re: [AMBER] The err of sander.PUPIL Joan Torras
- [AMBER] random number generators visible from nab: choice necessary? M. L. Dodson
- Re: [AMBER] random number generators visible from nab: choice necessary? case
- Re: [AMBER] random number generators visible from nab: choice necessary? M. L. Dodson
- [AMBER] Fwd: MMPBSA problem binding energy calculation kamlesh sahu
- Re: [AMBER] Fwd: MMPBSA problem binding energy calculation Bill Ross
- Re: [AMBER] Fwd: MMPBSA problem binding energy calculation Sushil Mishra
Tuesday, 8 June 2010
- [AMBER] GAFF 1.4 Masahiro HIGASHI
- [AMBER] How to modify config.h if I cannot get g77 running? Pls kindly help. Catein Catherine
- [AMBER] Error on running ptraj tianyuan meng
- [AMBER] Regarding temperature accelerated MD Ramya Narasimhan
- [AMBER] comparing DeltaG, docking and IC50 vaibhav dixit
- Re: [AMBER] How to modify config.h if I cannot get g77 running? Pls kindly help. Jason Swails
- Re: [AMBER] Error on running ptraj case
- [AMBER] gcc44 compiler Steve Seibold
- Re: [AMBER] gcc44 compiler case
- [AMBER] is it possible to improve amino acids dihedral angles using Amber? Andrew Voronkov
- RE: [AMBER] gcc44 compiler Steve Seibold
- [AMBER] Re: FW: Requesting your help in amber Jenny Iskrenova
- Re: [AMBER] Re: FW: Requesting your help in amber Jason Swails
- [AMBER] nfft1-3 too large! check on MAXNFFT in ew_bspline.f Ehsan Habibi
- Re: [AMBER] gcc44 compiler Lachele Foley (Lists)
- RE: [AMBER] gcc44 compiler Steve Seibold
- RE: [AMBER] How to modify config.h if I cannot get g77 running? Pls kindly help. Catein Catherine
- Re: [AMBER] nfft1-3 too large! check on MAXNFFT in ew_bspline.f case
- Re: [AMBER] Error on running ptraj Daniel Roe
- [AMBER] P450 ff from Rydberg et al. Renata KWIECIEN
- Re: [AMBER] random number generators visible from nab: choice necessary? M. L. Dodson
- [AMBER] how to cut phosphodiester bond Sangita Kachhap
- Re: [AMBER] about ewald error estimate Navanath Kumbhar
- [AMBER] pmemd.cuda error: launch timeout.. Sasha Buzko
- RE: [AMBER] pmemd.cuda error: launch timeout.. Scott Le Grand
- Re: [AMBER] pmemd.cuda error: launch timeout.. Sasha Buzko
- RE: [AMBER] pmemd.cuda error: launch timeout.. Scott Le Grand
- Re: [AMBER] pmemd.cuda error: launch timeout.. Sasha Buzko
- Re: [AMBER] nfft1-3 too large! check on MAXNFFT in ew_bspline.f Bill Ross
- RE: [AMBER] pmemd.cuda error: launch timeout.. Scott Le Grand
- Re: [AMBER] P450 ff from Rydberg et al. case
- Re: [AMBER] P450 ff from Rydberg et al. Adrian Roitberg
- Re: [AMBER] how to cut phosphodiester bond case
- Re: [AMBER] about ewald error estimate case
- [AMBER] SURFTEN / SURFOFF values are not consistent across *.all.out files Sushil Mishra
- Re: [AMBER] SURFTEN / SURFOFF values are not consistent across *.all.out files Dwight McGee
- [AMBER] free energy profile Lars Skjærven
- Re: [AMBER] SURFTEN / SURFOFF values are not consistent across *.all.out files Sushil Mishra
- RE: [AMBER] pmemd.cuda error: launch timeout.. Scott Le Grand
- Re: [AMBER] pmemd.cuda error: launch timeout.. Sasha Buzko
- RE: [AMBER] pmemd.cuda error: launch timeout.. Ross Walker
- [AMBER] solvent-solute interaction energy Hoshin Kim
- Re: [AMBER] solvent-solute interaction energy Bill Ross
- Re: [AMBER] solvent-solute interaction energy durmaz.zib.de
- Re: [AMBER] solvent-solute interaction energy Bill Ross
- Re: [AMBER] solvent-solute interaction energy Adrian Roitberg
- Re: [AMBER] pmemd.cuda error: launch timeout.. Sasha Buzko
Wednesday, 9 June 2010
- Re: [AMBER] free energy profile steinbrt.rci.rutgers.edu
- Re: [AMBER] solvent-solute interaction energy vedat durmaz
- Re: [AMBER] how to cut phosphodiester bond Sangita Kachhap
- Re: [AMBER] about ewald error estimate Navanath Kumbhar
- [AMBER] regarding forcefield for rna Asfa Ali
- [AMBER] antechamber failing with -mul option and sqm Alan
- Re: [AMBER] regarding forcefield for rna Gustavo Seabra
- [AMBER] Strange results for vaibhav dixit
- Re: [AMBER] regarding forcefield for rna Asfa Ali
- Re: [AMBER] regarding forcefield for rna InSuk Joung
- Re: [AMBER] regarding forcefield for rna Asfa Ali
- Re: [AMBER] regarding forcefield for rna Monika Sharma
- Re: [AMBER] regarding forcefield for rna InSuk Joung
- [AMBER] PTRAJ: setting up donor and acceptor masks for ligands for hbond analysis George Tzotzos
- Re: [AMBER] regarding forcefield for rna Jason Swails
- Re: [AMBER] regarding forcefield for rna Asfa Ali
- Re: [AMBER] regarding forcefield for rna Asfa Ali
- [AMBER] simple question, FATAL: Atom .R<NGLU 1>.A<H 18> does not have a type. Andrew Voronkov
- Re: [AMBER] regarding forcefield for rna Ilyas Yildirim
- [AMBER] question about radial distribution function Ganesh Kamath
- [AMBER] how to get frcmod.mod_phipsi.1 for constant pH MD simulation Sangita Kachhap
- [AMBER] Installing amber10 on ubunta, some hints please. Catein Catherine
- Re: [AMBER] how to get frcmod.mod_phipsi.1 for constant pH MD simulation Jason Swails
- Re: [AMBER] Installing amber10 on ubunta, some hints please. Jason Swails
- Re: [AMBER] simple question, FATAL: Atom .R<NGLU 1>.A<H 18> does not have a type. Jason Swails
- Re: [AMBER] Installing amber10 on ubunta, some hints please. Paul S. Nerenberg
- Re: [AMBER] Installing amber10 on ubunta, some hints please. Ye MEI
- Re: [AMBER] how to get frcmod.mod_phipsi.1 for constant pH MD simulation Sangita Kachhap
- Re: [AMBER] regarding forcefield for rna Bill Ross
- Re: [AMBER] simple question, FATAL: Atom .R<NGLU 1>.A<H 18> does not have a type. Bill Ross
- Re: [AMBER] how to get frcmod.mod_phipsi.1 for constant pH MD simulation Jason Swails
- RE: [AMBER] Installing amber10 on ubunta, some hints please. David Dubins
- [AMBER] MMPBSA binding calculations shenna shearin
- Re: [AMBER] MMPBSA binding calculations Jason Swails
- Re: [AMBER] free energy profile Lars Skjærven
- Re: [AMBER] regarding forcefield for rna case
- Re: [AMBER] antechamber failing with -mul option and sqm case
- Re: [AMBER] How to restart the remd simulation following the remd tutorial? Dongshan Wei
- [AMBER] Error while compiling AT1.4 on OS X Gustaf Olsson
Thursday, 10 June 2010
- Re: [AMBER] free energy profile steinbrt.rci.rutgers.edu
- [AMBER] ambertools1.2 compilation error colvin
- Re: [AMBER] ambertools1.2 compilation error Gustaf Olsson
- Re: [AMBER] ambertools1.2 compilation error colvin
- Re: [AMBER] ambertools1.2 compilation error Gustaf Olsson
- Re: [AMBER] ambertools1.2 compilation error colvin
- Re: [AMBER] ambertools1.2 compilation error Gustaf Olsson
Wednesday, 9 June 2010
- Re: [AMBER] regarding forcefield for rna Jiri Sponer
- Re: [AMBER] regarding forcefield for rna Jiri Sponer
Thursday, 10 June 2010
- Re: [AMBER] Error while compiling AT1.4 on OS X case
- Re: [AMBER] Error while compiling AT1.4 on OS X Gustaf Olsson
- Re: [AMBER] Error while compiling AT1.4 on OS X Gustaf Olsson
- Re: [AMBER] simple question, FATAL: Atom .R<NGLU 1>.A<H 18> does not have a type. Andrew Voronkov
- [AMBER] Building a slab between two vacuums? Gustaf Olsson
- Re: [AMBER] simple question, FATAL: Atom .R<NGLU 1>.A<H 18> does not have a type. Andrew Voronkov
- [AMBER] DNA analysis ros
- Re: [AMBER] regarding forcefield for rna Asfa Ali
- Re: [AMBER] regarding forcefield for rna Jiri Sponer
- Re: [AMBER] regarding forcefield for rna Jiri Sponer
- [AMBER] about sybylmol2 file Navanath Kumbhar
- [AMBER] 2drms Beale, John
- [AMBER] MMPBSA.py nmode maxcyc problem Niel Henriksen
- Re: [AMBER] 2drms Niel Henriksen
- Re: [AMBER] how to get frcmod.mod_phipsi.1 for constant pH MD simulation Sangita Kachhap
- [AMBER] Can I neglect the error message of sleap in amber tool? Catein Catherine
- Re: [AMBER] DNA analysis Robert Elder
- [AMBER] pmemd.cuda DPDP performance on GTX480 vs C2050? Sasha Buzko
- Re: [AMBER] Error while compiling AT1.4 on OS X Bill Ross
- Re: [AMBER] simple question, FATAL: Atom .R<NGLU 1>.A<H 18> does not have a type. Bill Ross
- [AMBER] info on ff10? Sidney Elmer
- Re: [AMBER] Building a slab between two vacuums? Bill Ross
- Re: [AMBER] simple question, FATAL: Atom .R<NGLU 1>.A<H 18> does not have a type. Bill Ross
- Re: [AMBER] regarding forcefield for rna Bill Ross
- [AMBER] Stuck on pmemd.f90 Paul Go
- [AMBER] RESP fit calculation Valerie Fako
- Re: [AMBER] regarding forcefield for rna Jiri Sponer
- Re: [AMBER] Error while compiling AT1.4 on OS X Gustaf Olsson
- Re: [AMBER] Can I neglect the error message of sleap in amber tool? Gustaf Olsson
- Re: [AMBER] pmemd.cuda segmentation fault with iwrap=1 on NVT/NVE Levi Pierce
- Re: [AMBER] pmemd.cuda segmentation fault with iwrap=1 on NVT/NVE Sasha Buzko
- Re: [AMBER] pmemd.cuda segmentation fault with iwrap=1 on NVT/NVE Levi Pierce
- [AMBER] Solute and solvent temperatures in mden Mickey Richards
- Re: [AMBER] Solute and solvent temperatures in mden Adrian Roitberg
- Re: [AMBER] Solute and solvent temperatures in mden Bill Ross
- Re: [AMBER] Solute and solvent temperatures in mden Mickey Richards
- Re: [AMBER] MMPBSA.py nmode maxcyc problem Jason Swails
- Re: [AMBER] MMPBSA.py nmode maxcyc problem Jason Swails
- Re: [AMBER] about sybylmol2 file Jason Swails
- Re: [AMBER] Stuck on pmemd.f90 Jason Swails
- Re: [AMBER] about sybylmol2 file case
- Re: [AMBER] simple question, FATAL: Atom .R<NGLU 1>.A<H 18> does not have a type. case
- Re: [AMBER] DNA analysis case
- Re: [AMBER] Can I neglect the error message of sleap in amber tool? case
- Re: [AMBER] info on ff10? case
- Re: [AMBER] Stuck on pmemd.f90 case
- Re: [AMBER] 2drms case
- Re: [AMBER] Solute and solvent temperatures in mden case
- Re: [AMBER] ambertools1.2 compilation error case
- Re: [AMBER] regarding forcefield for rna Bill Ross
- Re: [AMBER] Can I neglect the error message of sleap in amber tool? Here is my OS and compiler information. please kindly help. Catein Catherine
- Re: [AMBER] Can I neglect the error message of sleap in amber tool? Here is my OS and compiler information. please kindly help. Jason Swails
- Re: [AMBER] RESP fit calculation FyD
- Re: [AMBER] MMPBSA.py nmode maxcyc problem Jason Swails
- [AMBER] correlation luzhenw1.msu.edu
- Re: [AMBER] ambertools1.2 compilation error colvin
Friday, 11 June 2010
- [AMBER] reduce George Tzotzos
- [AMBER] simulation of DNA-protein interaction Ehsan Habibi
- [AMBER] Conserving water bridges? Waqas Nasir
- Re: [AMBER] Conserving water bridges? steinbrt.rci.rutgers.edu
- Re: [AMBER] about sybylmol2 file Navanath Kumbhar
- Re: [AMBER] regarding forcefield for rna Jiri Sponer
- Re: [AMBER] regarding forcefield for rna Asfa Ali
- Re: [AMBER] regarding forcefield for rna Jiri Sponer
- Re: [AMBER] ambertools1.2 compilation error case
- Re: [AMBER] Can I neglect the error message of sleap in amber tool? Here is my OS and compiler information. please kindly help. case
- Re: [AMBER] ambertools1.2 compilation error xueping chin
- Re: [AMBER] about sybylmol2 file FyD
- Re: [AMBER] reduce case
- Re: [AMBER] about sybylmol2 file case
- [AMBER] correlation matrix in PTRAJ luzhenw1.msu.edu
- Re: [AMBER] pmemd.cuda DPDP performance on GTX480 vs C2050? Ross Walker
- Re: [AMBER] Strange results for Bill Miller III
- Re: [AMBER] regarding forcefield for rna Bill Ross
- [AMBER] Invitation to connect on LinkedIn hyma srinivas
- [AMBER] protonation states of histidines - is there any way to treat it accurately. Andrew Voronkov
- [AMBER] Amber10 installation problem in linux Sangita Kachhap
- Re: [AMBER] pmemd.cuda DPDP performance on GTX480 vs C2050? Scott Le Grand
- Re: [AMBER] Conserving water bridges? Jason Swails
- Re: [AMBER] Amber10 installation problem in linux Mark Williamson
- Re: [AMBER] protonation states of histidines - is there any way to treat it accurately. Jason Swails
- Re: [AMBER] pmemd.cuda DPDP performance on GTX480 vs C2050? Sasha Buzko
- [AMBER] Can mm-pbsa be limited to simulating a fragment of a large protein? Sasha Buzko
- [AMBER] Lennard Jones calculation Antonios Samiotakis
- [AMBER] Modifying the bond energy calculation - adding a cubic bond term (hacking the sander code) Eric Shamay
- Re: [AMBER] Lennard Jones calculation case
- Re: [AMBER] random number generators visible from nab: choice necessary? case
- Re: [AMBER] Lennard Jones calculation Antonios Samiotakis
- Re: [AMBER] regarding forcefield for rna Asfa Ali
Saturday, 12 June 2010
- Re: [AMBER] about sybylmol2 file Navanath Kumbhar
- [AMBER] torsion angle define Navanath Kumbhar
- Re: [AMBER] torsion angle define Ilyas Yildirim
- Re: [AMBER] about sybylmol2 file case
- Re: [AMBER] torsion angle define Navanath Kumbhar
- Re: [AMBER] torsion angle define Ilyas Yildirim
- [AMBER] Postdoc position available at SDSC. Ross Walker
- Re: [AMBER] Lennard Jones calculation Antonios Samiotakis
- [AMBER] CUDA (GPU): Implementation does not support extra points. ashutosh shandilya
- Re: [AMBER] CUDA (GPU): Implementation does not support extra points. Ross Walker
- Re: [AMBER] torsion angle define Bill Ross
- Re: [AMBER] torsion angle define Bill Ross
- Re: [AMBER] about sybylmol2 file Bill Ross
- Re: [AMBER] torsion angle define Bill Ross
- Re: [AMBER] regarding forcefield for rna Bill Ross
- Re: [AMBER] MMPBSA binding calculations shenna shearin
- Re: [AMBER] MMPBSA binding calculations shenna shearin
- Re: [AMBER] MMPBSA binding calculations Jason Swails
- Re: [AMBER] MMPBSA binding calculations shenna shearin
- Re: [AMBER] MMPBSA binding calculations shenna shearin
- Re: [AMBER] MMPBSA binding calculations Bill Miller III
- Re: [AMBER] MMPBSA binding calculations shenna shearin
Sunday, 13 June 2010
- [AMBER] (no subject) Catein Catherine
- [AMBER] Can I did MM/GBSA analysis for a partial equilibrated system? Catein Catherine
- [AMBER] Why different results were obtained for two runs using the same prmtop files? Catein Catherine
- [AMBER] constant pH simulation (protonation state specification) Sangita Kachhap
- Re: [AMBER] constant pH simulation (protonation state specification) Jason Swails
- Re: [AMBER] (no subject) Jason Swails
- Re: [AMBER] Can I did MM/GBSA analysis for a partial equilibrated system? Jason Swails
- Re: [AMBER] constant pH simulation (protonation state specification) Sangita Kachhap
- Re: [AMBER] regarding forcefield for rna Asfa Ali
- Re: [AMBER] CUDA (GPU): Implementation does not support extra points. ashutosh shandilya
- Re: [AMBER] constant pH simulation (protonation state specification) Jason Swails
Monday, 14 June 2010
- [AMBER] antechamber monica.imtech.res.in
- [AMBER] Ptraj problems Samuel Genheden
- Re: [AMBER] Ptraj problems Thomas Cheatham
- [AMBER] Free Energy profile Anna Reymer
- Re: [AMBER] Conserving water bridges? need help... Waqas Nasir
- Re: [AMBER] Ptraj problems Samuel Genheden
- Re: [AMBER] Conserving water bridges? need help... steinbrt.rci.rutgers.edu
- Re: [AMBER] CUDA (GPU): Implementation does not support extra points. case
- [AMBER] parallel compiling failure of Amber 11 Yubo Fan
- [AMBER] visualising frame of minimisation Alan
- [AMBER] MMPBSA.py error George Tzotzos
- Re: [AMBER] parallel compiling failure of Amber 11 Ross Walker
- Re: [AMBER] parallel compiling failure of Amber 11 case
- Re: [AMBER] Conserving water bridges? need help... Bill Ross
- Re: [AMBER] MMPBSA.py error Dwight McGee
- Re: [AMBER] MMPBSA.py error Jason Swails
- [AMBER] peptide leaving box, image command not working Omair A. Khan
- Re: [AMBER] pmemd.cuda DPDP performance on GTX480 vs C2050? Sasha Buzko
- Re: [AMBER] pmemd.cuda DPDP performance on GTX480 vs C2050? michael bane
- Re: [AMBER] pmemd.cuda DPDP performance on GTX480 vs C2050? Ross Walker
- Re: [AMBER] pmemd.cuda DPDP performance on GTX480 vs C2050? Ross Walker
- Re: [AMBER] pmemd.cuda DPDP performance on GTX480 vs C2050? Scott Le Grand
- Re: [AMBER] pmemd.cuda DPDP performance on GTX480 vs C2050? Ross Walker
- [AMBER] forrtl: severe (64): input conversion error, unit 9, file Homa Azizian
- [AMBER] About md parameters for unuaual amino acid residues Rilei Yu
- [AMBER] about atom type Navanath Kumbhar
- Re: [AMBER] forrtl: severe (64): input conversion error, unit 9, file Jason Swails
- Re: [AMBER] About md parameters for unuaual amino acid residues Jason Swails
- Re: [AMBER] MMPBSA.py error George Tzotzos
- [AMBER] want to keep water from the pdb vaibhav dixit
- Re: [AMBER] MMPBSA.py error Jason Swails
Tuesday, 15 June 2010
- Re: [AMBER] want to keep water from the pdb Jason Swails
- Re: [AMBER] About md parameters for unuaual amino acid residues Rilei Yu
- [AMBER] Polarizability and induced dipoles Mag. Thomas Taylor
- Re: [AMBER] Polarizability and induced dipoles Ross Walker
- Re: [AMBER] want to keep water from the pdb vaibhav dixit
- [AMBER] how can i run min.in heat.in density.in equil.in as one sander job? vaibhav dixit
- [AMBER] nmr refinment problem shirishkumar pawar
- [AMBER] plz help!!! monica.imtech.res.in
- Re: [AMBER] Polarizability and induced dipoles Mag. Thomas Taylor
- Re: [AMBER] how can i run min.in heat.in density.in equil.in as one sander job? Gustavo Seabra
- Re: [AMBER] plz help!!! Nicee
- [AMBER] to understand 1-4 interactions in Amber FF Alan
- [AMBER] problems with NAB and SHIFTS Jakob Toudahl Nielsen
- Re: [AMBER] Polarizability and induced dipoles Ross Walker
- Re: [AMBER] to understand 1-4 interactions in Amber FF Ross Walker
- Re: [AMBER] problems with NAB and SHIFTS Jason Swails
- Re: [AMBER] to understand 1-4 interactions in Amber FF Alan
- Re: [AMBER] problems with NAB and SHIFTS Jakob Toudahl Nielsen
- Re: [AMBER] problems with NAB and SHIFTS case
- Re: [AMBER] nmr refinment problem case
- Re: [AMBER] problems with NAB and SHIFTS Jakob Toudahl Nielsen
- Re: [AMBER] constant pH simulation (syn and anti position) Sangita Kachhap
- Re: [AMBER] peptide leaving box, image command not working Niel Henriksen
- Re: [AMBER] problems with NAB and SHIFTS case
- Re: [AMBER] about atom type case
- Re: [AMBER] forrtl: severe (64): input conversion error, unit 9, file Bill Ross
- Re: [AMBER] want to keep water from the pdb Bill Ross
- Re: [AMBER] to understand 1-4 interactions in Amber FF Bill Ross
- [AMBER] MD simulation of methylated DNA: addition of methyl groups to .pdb file Ehsan Habibi
- Re: [AMBER] MD simulation of methylated DNA: addition of methyl groups to .pdb file Bill Ross
- Re: [AMBER] problems with NAB and SHIFTS Jakob Toudahl Nielsen
- Re: [AMBER] MD simulation of methylated DNA: addition of methyl groups to .pdb file case
- Re: [AMBER] problems with NAB and SHIFTS Bill Ross
- Re: [AMBER] problems with NAB and SHIFTS Eric Shamay
- Re: [AMBER] problems with NAB and SHIFTS Jason Swails
- Re: [AMBER] problems with NAB and SHIFTS case
- [AMBER] picky nab compiler: is this really necessary? M. L. Dodson
- Re: [AMBER] density John S
- Re: [AMBER] nmr refinment problem shirishkumar pawar
- [AMBER] Rdf and density John S
- [AMBER] pH based conformational study Sangita Kachhap
Wednesday, 16 June 2010
- [AMBER] sietraj Yossa Dwi Hartono
- Re: [AMBER] problems with NAB and SHIFTS Jakob Toudahl Nielsen
- Re: [AMBER] how can i run min.in heat.in density.in equil.in as one sander job? vaibhav dixit
- [AMBER] frcdump for CHARMM Mag. Thomas Taylor
- Re: [AMBER] how can i run min.in heat.in density.in equil.in as one sander job? Gustavo Seabra
- Re: [AMBER] frcdump for CHARMM Ross Walker
- Re: [AMBER] how can i run min.in heat.in density.in equil.in as one sander job? Ross Walker
- [AMBER] amber10 installation problem Devlina Chakravarty
- Re: [AMBER] problems with NAB and SHIFTS Jason Swails
- Re: [AMBER] pH based conformational study Jason Swails
- Re: [AMBER] pH based conformational study Sangita Kachhap
- Re: [AMBER] problems with NAB and SHIFTS case
- Re: [AMBER] sietraj Purisima, Enrico
- [AMBER] MMPBSA : SA Bomb in sa_arc : Allocation aborted error Cristina Sisu
- [AMBER] FW: frcdump for CHARMM Ross Walker
- [AMBER] ptraj rms error Beale, John
- Re: [AMBER] picky nab compiler: is this really necessary? case
- Re: [AMBER] amber10 installation problem case
- Re: [AMBER] picky nab compiler: is this really necessary? M. L. Dodson
- Re: [AMBER] MMPBSA : SA Bomb in sa_arc : Allocation aborted error Ray Luo
- Re: [AMBER] ptraj rms error Daniel Roe
- Re: [AMBER] picky nab compiler: is this really necessary? case
- [AMBER] high bidning energy MMPBSA kamlesh sahu
- Re: [AMBER] high bidning energy MMPBSA Bill Miller III
- [AMBER] Fwd: high bidning energy MMPBSA kamlesh sahu
- Re: [AMBER] high bidning energy MMPBSA kamlesh sahu
- Re: [AMBER] high bidning energy MMPBSA kamlesh sahu
- Re: [AMBER] high bidning energy MMPBSA Jason Swails
- Re: [AMBER] high bidning energy MMPBSA Bill Miller III
- Re: [AMBER] high bidning energy MMPBSA kamlesh sahu
- Re: [AMBER] Creating topology files for protein-ligand complex case
- [AMBER] problem with the energetics of the system Homa Azizian
- Re: [AMBER] problem with the energetics of the system Gustavo Seabra
- Re: [AMBER] Creating topology files for protein-ligand complex Heather Condurso
- Re: [AMBER] problem with the energetics of the system Homa Azizian
- Re: [AMBER] problem with the energetics of the system Bill Ross
- Re: [AMBER] problem with the energetics of the system Bill Ross
- Re: [AMBER] sietraj Yossa Dwi Hartono
Thursday, 17 June 2010
- Re: [AMBER] amber10 installation problem Indrajit Deb
- Re: [AMBER] amber10 installation problem Sudeep Narayan Banerjee
- [AMBER] rhombicity Peter Podbevšek
- Re: [AMBER] ptraj rms error Beale, John
- Re: [AMBER] ptraj rms error Beale, John
- Re: [AMBER] visualising frame of minimisation Jason Swails
- Re: [AMBER] ptraj rms error case
- [AMBER] Parameters for Nickel Dian Jiao
- Re: [AMBER] Parameters for Nickel Jason Swails
- [AMBER] What's the mean of this ptraj error message? thanks in advance. Catein Catherine
- Re: [AMBER] What's the mean of this ptraj error message? thanks in advance. Jason Swails
- Re: [AMBER] What's the mean of this ptraj error message? thanks in advance. Paul S. Nerenberg
- [AMBER] bond angle and distance calculation Hoshin Kim
- [AMBER] Solvation free energy of a capped 9mer peptide Lekpa Duukori
- Re: [AMBER] Solvation free energy of a capped 9mer peptide Ray Luo
- Re: [AMBER] problem with the energetics of the system Homa Azizian
- Re: [AMBER] problem with the energetics of the system Jason Swails
- Re: [AMBER] rhombicity case
Friday, 18 June 2010
- [AMBER] MMPBSA warning George Tzotzos
- [AMBER] mmpbsa RANAJIT SHINDE
- [AMBER] a query about analysis oguz gurbulak
- Re: [AMBER] mmpbsa Jason Swails
- Re: [AMBER] MMPBSA warning Jason Swails
- Re: [AMBER] a query about analysis Jason Swails
- [AMBER] PBC in umbrella sampling dhacademic
- Re: [AMBER] problem with the energetics of the system Bill Ross
Thursday, 17 June 2010
- [AMBER] bond angle and distance problem Hoshin Kim
Friday, 18 June 2010
- [AMBER] radial distribution function Ganesh Kamath
- Re: [AMBER] PBC in umbrella sampling case
- [AMBER] how to use a distant-dependent dielectric constant of "epsilon = 4r" DeChang Li
- [AMBER] antechamber issue and parameters for heme of cyp3a4 vaibhav dixit
- Re: [AMBER] mmpbsa RANAJIT SHINDE
- Re: [AMBER] problem with the energetics of the system Homa Azizian
- [AMBER] graphical analysis of H-bond Homa Azizian
Saturday, 19 June 2010
- [AMBER] constant pH equilibration confusion Sangita Kachhap
- Re: [AMBER] constant pH equilibration confusion manikanthan bhavaraju
- Re: [AMBER] how to use a distant-dependent dielectric constant of "epsilon = 4r" case
- Re: [AMBER] Lennard Jones calculation case
- Re: [AMBER] constant pH equilibration confusion Jason Swails
- Re: [AMBER] problem with the energetics of the system Jason Swails
- Re: [AMBER] problem with the energetics of the system Bill Ross
- Re: [AMBER] constant pH equilibration confusion Bill Ross
- Re: [AMBER] antechamber issue and parameters for heme of cyp3a4 Jio M
- Re: [AMBER] constant pH equilibration confusion Sangita Kachhap
- Re: [AMBER] constant pH equilibration confusion Jason Swails
- Re: [AMBER] constant pH equilibration confusion Sangita Kachhap
- Re: [AMBER] constant pH equilibration confusion Sangita Kachhap
- Re: [AMBER] problem with the energetics of the system case
- Re: [AMBER] constant pH equilibration confusion Jason Swails
- Re: [AMBER] constant pH equilibration confusion Jason Swails
- Re: [AMBER] constant pH equilibration confusion Bill Ross
- [AMBER] two questions about Amber annealing Yiyu Li
- Re: [AMBER] two questions about Amber annealing Bill Ross
- Re: [AMBER] antechamber issue and parameters for heme of cyp3a4 vaibhav dixit
- Re: [AMBER] two questions about Amber annealing Ross Walker
- [AMBER] Query- Heating after Equilibration Jagdeesh C
Sunday, 20 June 2010
- Re: [AMBER] two questions about Amber annealing Bill Ross
- [AMBER] "prepin", ".frcmod" and "pdb" files of 5-methylcytidine (for DNA (dC) no RNA) Ehsan Habibi
- Re: [AMBER] Query- Heating after Equilibration case
- Re: [AMBER] Query- Heating after Equilibration Jason Swails
- [AMBER] xleap problem for terminal DNA base pairs. Catein Catherine
- Re: [AMBER] xleap problem for terminal DNA base pairs. Jason Swails
- [AMBER] Is xleap part of Ambertool or Amber10? Catein Catherine
- [AMBER] Is AmberTools 1.4 compatible with AMBER10? Catein Catherine
- Re: [AMBER] Is xleap part of Ambertool or Amber10? Jason Swails
- Re: [AMBER] Is AmberTools 1.4 compatible with AMBER10? Jason Swails
- Re: [AMBER] xleap problem for terminal DNA base pairs. Bill Ross
- [AMBER] Is it a bug in the xleap of AmberTools 1.2 and 1.4. Catein Catherine
Monday, 21 June 2010
- Re: [AMBER] a query about analysis Cenk \(Jenk\) Andac
- [AMBER] Problem with pmed installation: Amber 10 Devlina Chakravarty
- [AMBER] constant pH simulation ERROR "vlimit exceeded for step" Sangita Kachhap
- Re: [AMBER] Is it a bug in the xleap of AmberTools 1.2 and 1.4. case
- Re: [AMBER] Problem with pmed installation: Amber 10 Jason Swails
- Re: [AMBER] constant pH simulation ERROR "vlimit exceeded for step" Jason Swails
- Re: [AMBER] Problem with pmed installation: Amber 10 Ross Walker
- Re: [AMBER] constant pH simulation ERROR "vlimit exceeded for step" Sangita Kachhap
- Re: [AMBER] constant pH simulation ERROR "vlimit exceeded for step" Jason Swails
- Re: [AMBER] constant pH simulation ERROR "vlimit exceeded for step" Sangita Kachhap
- [AMBER] unexpected "vlimit exceeded for step" error Cristina Sisu
- Re: [AMBER] unexpected "vlimit exceeded for step" error case
- Re: [AMBER] unexpected "vlimit exceeded for step" error Ross Walker
- Re: [AMBER] parallel compiling failure of Amber 11 Yubo Fan
- Re: [AMBER] parallel compiling failure of Amber 11 Jason Swails
- [AMBER] periodic images of truc. octahedron in vmd Paul Brandt
- Re: [AMBER] periodic images of truc. octahedron in vmd Bill Ross
- Re: [AMBER] periodic images of truc. octahedron in vmd Paul Brandt
- Re: [AMBER] periodic images of truc. octahedron in vmd Paul Brandt
- Re: [AMBER] parallel compiling failure of Amber 11 Yubo Fan
- [AMBER] (no subject) moitrayee.mbu.iisc.ernet.in
- [AMBER] center and image Homa Azizian
Tuesday, 22 June 2010
- Re: [AMBER] parallel compiling failure of Amber 11 Gustavo Seabra
- [AMBER] improper for NH2 group in guanosine Dmitry Nilov
- Re: [AMBER] unexpected "vlimit exceeded for step" error Cristina Sisu
- Re: [AMBER] center and image Jason Swails
- [AMBER] Unknown clustering algorithm_ptraj_ambertools1.4 moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] Unknown clustering algorithm_ptraj_ambertools1.4 Dwight McGee
- Re: [AMBER] parallel compiling failure of Amber 11 Yubo Fan
- Re: [AMBER] Unknown clustering algorithm_ptraj_ambertools1.4 Fredrick Devadoss
- Re: [AMBER] parallel compiling failure of Amber 11 Jason Swails
- [AMBER] How to read the motion of PCA? Catein Catherine
- Re: [AMBER] unexpected "vlimit exceeded for step" error Ross Walker
- [AMBER] about alanine scanning lidansa.mail.ustc.edu.cn
- Re: [AMBER] parallel compiling failure of Amber 11 Yubo Fan
- [AMBER] how to modify the code to save the trajectory of ONLY one part of atoms in .mdcrd file ? Dongshan Wei
- Re: [AMBER] Is it a bug in the xleap of AmberTools 1.2 and 1.4. Catein Catherine
- Re: [AMBER] about alanine scanning Sushil Mishra
- Re: [AMBER] parallel compiling failure of Amber 11 Jason Swails
- Re: [AMBER] about alanine scanning Dwight McGee
- Re: [AMBER] how to modify the code to save the trajectory of ONLY one part of atoms in .mdcrd file ? Jason Swails
- Re: [AMBER] how to modify the code to save the trajectory of ONLY one part of atoms in .mdcrd file ? Jason Swails
- Re: [AMBER] unexpected "vlimit exceeded for step" error Bill Ross
- Re: [AMBER] parallel compiling failure of Amber 11 Yubo Fan
- [AMBER] radial distribution function in amber Ganesh Kamath
- Re: [AMBER] unexpected "vlimit exceeded for step" error Cristina Sisu
- Re: [AMBER] unexpected "vlimit exceeded for step" error Bill Ross
- [AMBER] constant pH simulation ERROR "vlimit exceeded for step" Sangita Kachhap
- Re: [AMBER] constant pH simulation ERROR "vlimit exceeded for step" Bill Ross
- Re: [AMBER] constant pH simulation ERROR "vlimit exceeded for step" Sangita Kachhap
- [AMBER] antechamber/gasteiger problem with FMN Eric Pettersen
- Re: [AMBER] antechamber/gasteiger problem with FMN Eric Pettersen
- Re: [AMBER] how to modify the code to save the trajectory of ONLY one part of atoms in .mdcrd file ? Gustavo Seabra
- Re: [AMBER] constant pH simulation ERROR "vlimit exceeded for step" Sangita Kachhap
- Re: [AMBER] constant pH simulation ERROR "vlimit exceeded for step" Bill Ross
- Re: [AMBER] constant pH simulation ERROR "vlimit exceeded for step" Sangita Kachhap
- Re: [AMBER] constant pH simulation ERROR "vlimit exceeded for step" Bill Ross
- Re: [AMBER] Is it a bug in the xleap of AmberTools 1.2 and 1.4. case
- Re: [AMBER] improper for NH2 group in guanosine case
- Re: [AMBER] how to modify the code to save the trajectory of ONLY one part of atoms in .mdcrd file ? Dongshan Wei
- Re: [AMBER] about alanine scanning lidansa.mail.ustc.edu.cn
- [AMBER] stripping water Homa Azizian
- Re: [AMBER] parallel compiling failure of Amber 11 Yubo Fan
- [AMBER] stripping water and cross-correlation analysis Homa Azizian
- Re: [AMBER] parallel compiling failure of Amber 11 Jason Swails
- Re: [AMBER] Query- Heating after Equilibration Jagdeesh C
- Re: [AMBER] stripping water and cross-correlation analysis case
- Re: [AMBER] parallel compiling failure of Amber 11 case
- Re: [AMBER] Query- Heating after Equilibration case
- [AMBER] speed of analysis Homa Azizian
- Re: [AMBER] parallel compiling failure of Amber 11 Bill Ross
- Re: [AMBER] speed of analysis Ross Walker
- Re: [AMBER] Query- Heating after Equilibration Bill Ross
- Re: [AMBER] stripping water Ross Walker
- [AMBER] simulating in urea monica.imtech.res.in
- Re: [AMBER] constant pH simulation ERROR "vlimit exceeded for step" Sangita Kachhap
- Re: [AMBER] about alanine scanning Sushil Mishra
Wednesday, 23 June 2010
- Re: [AMBER] about alanine scanning lidansa.mail.ustc.edu.cn
- Re: [AMBER] improper for NH2 group in guanosine Dmitry Nilov
- [AMBER] dna monica.imtech.res.in
- Re: [AMBER] How to read the motion of PCA? Hannes Loeffler
- Re: [AMBER] unexpected "vlimit exceeded for step" error Cristina Sisu
- Re: [AMBER] Query- Heating after Equilibration Jagdeesh C
- [AMBER] dna Kevin Hauser
- Re: [AMBER] simulating in urea case
- [AMBER] pre-processing of trajectories moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] dna case
- Re: [AMBER] pre-processing of trajectories Hannes Loeffler
- [AMBER] restraint during constant pH Sangita Kachhap
- Re: [AMBER] restraint during constant pH Jason Swails
- Re: [AMBER] simulating in urea monica.imtech.res.in
- Re: [AMBER] dna monica.imtech.res.in
- Re: [AMBER] simulating in urea case
- Re: [AMBER] dna case
- Re: [AMBER] dna Kevin Hauser
- [AMBER] Ptraj error - ERROR in safe_malloc Siddharth Rastogi
- Re: [AMBER] unexpected "vlimit exceeded for step" error Ross Walker
- [AMBER] MMPBSA.py install problem Oliver Grant
- Re: [AMBER] restraint during constant pH Sangita Kachhap
- Re: [AMBER] simulating in urea Bill Ross
- Re: [AMBER] constant pH simulation ERROR "vlimit exceeded for step" Bill Ross
- Re: [AMBER] MMPBSA.py install problem Bill Miller III
- Re: [AMBER] unexpected "vlimit exceeded for step" error Bill Ross
- Re: [AMBER] restraint during constant pH Jason Swails
- Re: [AMBER] Ptraj error - ERROR in safe_malloc case
- Re: [AMBER] pre-processing of trajectories moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] pre-processing of trajectories hannes.loeffler.stfc.ac.uk
- Re: [AMBER] Ptraj error - ERROR in safe_malloc Siddharth Rastogi
- [AMBER] amberhome not set Ping
- Re: [AMBER] amberhome not set Heather Condurso
- Re: [AMBER] amberhome not set Bill Ross
- Re: [AMBER] amberhome not set Ping
- Re: [AMBER] amberhome not set Jason Swails
- [AMBER] How to build a TT dimer Shi Choong
- [AMBER] Restraint John S
- Re: [AMBER] restraint during constant pH Sangita Kachhap
- Re: [AMBER] restraint during constant pH Jason Swails
- Re: [AMBER] simulating in urea monica.imtech.res.in
- Re: [AMBER] simulating in urea monica.imtech.res.in
Thursday, 24 June 2010
- Re: [AMBER] pre-processing of trajectories moitrayee.mbu.iisc.ernet.in
- [AMBER] [Fwd: Re: pre-processing of trajectories] moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] pre-processing of trajectories Hannes Loeffler
- Re: [AMBER] unexpected "vlimit exceeded for step" error Cristina Sisu
- [AMBER] Kinetic energy after heating is zero Ashutosh Shandilya
- Re: [AMBER] Kinetic energy after heating is zero Jason Swails
- [AMBER] inter_intra - energy balaji nagarajan
- [AMBER] Error encounter when running tutorial 4b when running xleap with AMBER 10 and AmberTools 1.2 Catein Catherine
- Re: [AMBER] Error encounter when running tutorial 4b when running xleap with AMBER 10 and AmberTools 1.2 Jason Swails
- [AMBER] Can i use DA instead of DA3/DA5 for teminal residues? Catein Catherine
- Re: [AMBER] How to build a TT dimer M. L. Dodson
- Re: [AMBER] Kinetic energy after heating is zero case
- Re: [AMBER] Kinetic energy after heating is zero Jason Swails
- Re: [AMBER] Can i use DA instead of DA3/DA5 for teminal residues? case
- Re: [AMBER] Restraint case
- [AMBER] RESP charge of heavy metal contained complex Jia Xu
- [AMBER] AmberTool 1.4 ptraj error Steve Seibold
- [AMBER] intra-inter energy balaji nagarajan
- Re: [AMBER] Error encounter when running tutorial 4b when running xleap with AMBER 10 and AmberTools 1.2 Catein Catherine
- Re: [AMBER] Error encounter when running tutorial 4b when running xleap with AMBER 10 and AmberTools 1.2 Jason Swails
- [AMBER] AMBER11 and AmberTools1.4 errors Steve Seibold
- Re: [AMBER] AMBER11 and AmberTools1.4 errors Jason Swails
- [AMBER] (no subject) Steve Seibold
- Re: [AMBER] (no subject) Bill Ross
- Re: [AMBER] (no subject) Paul S. Nerenberg
- Re: [AMBER] (no subject) Paul S. Nerenberg
- [AMBER] (no subject) Steve Seibold
- Re: [AMBER] RESP charge of heavy metal contained complex FyD
Friday, 25 June 2010
- Re: [AMBER] pre-processing of trajectories monica.imtech.res.in
- Re: [AMBER] dna monica.imtech.res.in
- [AMBER] MMPBSA.py NameError: global name 'diffstdev' is not defined Oliver Grant
- [AMBER] Can't locate mm_pbsa_global.pm in .INC fancy2012
- Re: [AMBER] MMPBSA.py NameError: global name 'diffstdev' is not defined Oliver Grant
- Re: [AMBER] MMPBSA.py NameError: global name 'diffstdev' is not defined Jason Swails
- Re: [AMBER] Can't locate mm_pbsa_global.pm in .INC Jason Swails
- Re: [AMBER] pre-processing of trajectories Hannes Loeffler
- Re: [AMBER] dna case
- Re: [AMBER] MMPBSA.py NameError: global name 'diffstdev' is not defined Jason Swails
- [AMBER] Combine trajectory files error Steve Seibold
- Re: [AMBER] (no subject) shenna shearin
- [AMBER] AMBER, shenna shearin has invited you to open a Google mail account shenna shearin
- [AMBER] cluster analysis shenna shearin
- [AMBER] mme and mme2 produce different energies Kevin Wiehe
- [AMBER] Checksums? Marc Moreau
- Re: [AMBER] Checksums? Ross Walker
- [AMBER] ptraj (AT 1.4) hiccups with gzipped trajectory files Paul S. Nerenberg
- Re: [AMBER] pmemd.cuda segmentation fault with iwrap=1 on NVT/NVE Scott Le Grand
- Re: [AMBER] Can't locate mm_pbsa_global.pm in .INC fancy2012
- Re: [AMBER] pmemd.cuda segmentation fault with iwrap=1 on NVT/NVE Levi Pierce
Saturday, 26 June 2010
- [AMBER] Segmentation fault Jagdeesh C
- [AMBER] Constant protonation vs. constant pH simulation nicholus bhattacharjee
- Re: [AMBER] Constant protonation vs. constant pH simulation Adrian Roitberg
- Re: [AMBER] Constant protonation vs. constant pH simulation nicholus bhattacharjee
- Re: [AMBER] Constant protonation vs. constant pH simulation Jason Swails
- Re: [AMBER] Segmentation fault case
- Re: [AMBER] pre-processing of trajectories monica.imtech.res.in
- Re: [AMBER] dna monica.imtech.res.in
- Re: [AMBER] Segmentation fault Jagdeesh C
Sunday, 27 June 2010
- [AMBER] ptraj.MPI in Ambertools1.4 : Compression is not currently supported for parallel ptraj M. Reza Ganjalikhany
- Re: [AMBER] ptraj.MPI in Ambertools1.4 : Compression is not currently supported for parallel ptraj M. Reza Ganjalikhany
- [AMBER] mmpbsa installation rameshwar prajapati
- [AMBER] RMSD calculation per reside wise not rmse/time by ptraj REENU KHATTRI
- Re: [AMBER] RMSD calculation per reside wise not rmse/time by ptraj Jason Swails
- Re: [AMBER] mmpbsa installation Jason Swails
- Re: [AMBER] ptraj.MPI in Ambertools1.4 : Compression is not currently supported for parallel ptraj Jason Swails
- [AMBER] mmpbsa error of missing SVIB, when nm=0 Catein Catherine
- Re: [AMBER] dna Kevin Hauser
- Re: [AMBER] ptraj.MPI in Ambertools1.4 : Compression is not currently supported for parallel ptraj M. Reza Ganjalikhany
- Re: [AMBER] pre-processing of trajectories case
- [AMBER] is there any command to superimpose/align a protein in amber8 to get less RMSD residue wise REENU KHATTRI
- Re: [AMBER] pmemd.cuda segmentation fault with iwrap=1 on NVT/NVE case
- Re: [AMBER] [q4md-fft] Re: RESP charge of heavy metal contained complex Jia Xu
- [AMBER] reducing the fram for analysing Homa Azizian
- [AMBER] how to allign the protein with average pdb REENU KHATTRI
Monday, 28 June 2010
- [AMBER] inter- intra energy balaji nagarajan
- Re: [AMBER] how to allign the protein with average pdb Jason Swails
- Re: [AMBER] reducing the fram for analysing Jason Swails
- [AMBER] (no subject) Beale, John
- Re: [AMBER] (no subject) Emmanuel Baribefe Naziga
- [AMBER] Fwd: how to allign the protein with average pdb REENU KHATTRI
- Re: [AMBER] TUTORIAL A7 Replica Exchange Simulations with AMBER 10 Ross Walker
- [AMBER] solute ans solvation box Emmanuel Baribefe Naziga
- Re: [AMBER] ptraj (AT 1.4) hiccups with gzipped trajectory files Paul S. Nerenberg
- [AMBER] Errors in installing amber10 in cygwin (winxp) Yan Gao
- [AMBER] How to insert a dimer into the pdb file Shi Choong
- Re: [AMBER] Fwd: how to allign the protein with average pdb Jason Swails
- Re: [AMBER] Errors in installing amber10 in cygwin (winxp) case
- Re: [AMBER] dna case
- [AMBER] regarding ptraj Asfa Ali
Tuesday, 29 June 2010
- Re: [AMBER] regarding ptraj Gustavo Seabra
- [AMBER] force field parameter and resp charge calculation colvin
- [AMBER] Fwd: Fwd: how to allign the protein with average pdb REENU KHATTRI
- [AMBER] Compiling failure of Amber 9 Yubo Fan
- Re: [AMBER] Compiling failure of Amber 9 Jason Swails
- [AMBER] make test.parallel Steve Seibold
- Re: [AMBER] make test.parallel case
- Re: [AMBER] mme and mme2 produce different energies case
- Re: [AMBER] force field parameter and resp charge calculation FyD
- Re: [AMBER] regarding ptraj Bill Ross
- Re: [AMBER] (no subject) Thomas Cheatham III
- Re: [AMBER] Compiling failure of Amber 9 Yubo Fan
- Re: [AMBER] Compiling failure of Amber 9 Jason Swails
- [AMBER] similarity of quasi-harmonic modes dependent on reference conformation Jose Borreguero
- Re: [AMBER] similarity of quasi-harmonic modes dependent on reference conformation Jason Swails
- [AMBER] Questions with input file in constant pH MD nicholus bhattacharjee
- Re: [AMBER] [q4md-fft] Re: RESP charge of heavy metal contained complex FyD
- Re: [AMBER] force field parameter and resp charge calculation FyD
- Re: [AMBER] force field parameter and resp charge calculation xueping chin
- Re: [AMBER] force field parameter and resp charge calculation colvin
- Re: [AMBER] force field parameter and resp charge calculation FyD
Wednesday, 30 June 2010
- Re: [AMBER] force field parameter and resp charge calculation FyD
- Re: [AMBER] force field parameter and resp charge calculation colvin
- [AMBER] mmgbsa tricky output Amor San Juan
- Re: [AMBER] force field parameter and resp charge calculation FyD
- [AMBER] regarding mmpbsa Asfa Ali
- Re: [AMBER] make test.parallel Steve Seibold
- Re: [AMBER] similarity of quasi-harmonic modes dependent on reference conformation Jose Borreguero
- Re: [AMBER] regarding mmpbsa Bill Miller III
- Re: [AMBER] ptraj (AT 1.4) hiccups with gzipped trajectory files Daniel Roe
- Re: [AMBER] Questions with input file in constant pH MD Bill Miller III
- Re: [AMBER] force field parameter and resp charge calculation colvin
- Re: [AMBER] ptraj.MPI in Ambertools1.4 : Compression is not currently supported for parallel ptraj Daniel Roe
- Re: [AMBER] regarding mmpbsa Jason Swails
- Re: [AMBER] regarding mmpbsa Asfa Ali
- Re: [AMBER] force field parameter and resp charge calculation FyD
- Re: [AMBER] regarding mmpbsa Jason Swails
- Re: [AMBER] [q4md-fft] Re: RESP charge of heavy metal contained complex Jia Xu
- Re: [AMBER] Segmentation fault case
- [AMBER] Adding Ions. Ajay Ummat
- Re: [AMBER] Adding Ions. case
- Re: [AMBER] Adding Ions. Bill Ross
- Re: [AMBER] Adding Ions. Hugh Heldenbrand
- [AMBER] vlimit exceeded for step Le, Shu-Yun (NIH/NCI) [E]
- Re: [AMBER] vlimit exceeded for step Jason Swails
- Re: [AMBER] vlimit exceeded for step Bill Ross
- [AMBER] Any way to apply different dt(time/step) to different steps Yiyu Li
- [AMBER] adding counterions Ping
- [AMBER] AmberTools installation in Cygwin Yan Gao
- [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o Yu Chen
- Re: [AMBER] Any way to apply different dt(time/step) to different steps Daniel Roe
- Re: [AMBER] Adding Ions. Dean Cuebas

Last message date: Wed Jun 30 2010 - 22:00:03 PDT
Archived on: Fri Apr 26 2024 - 05:54:07 PDT

Amber Archive Jun 2010 by date