Amber Archive Nov 2014: by date

Saturday, 1 November 2014
- [AMBER] Calculating Normalised electron density for DOPC. Him Shweta
- Re: [AMBER] [q4md-fft] FAD wrong geometry in F-90 project FyD
- Re: [AMBER] Problem regarding Chamber and psf file Jason Swails
- [AMBER] Fwd: Re: [q4md-fft] FAD wrong geometry in F-90 project FyD
Sunday, 2 November 2014
- Re: [AMBER] restart file position Fabian Glaser
- Re: [AMBER] restart file position Jason Swails
- Re: [AMBER] Problem regarding Chamber and psf file Pete Kekenes-Huskey
- Re: [AMBER] NVT and NPT ensemble Sangita Kachhap
Monday, 3 November 2014
- [AMBER] Fully random MPI error after updating CentOS from release 6.5 to 6.6 Massimiliano Porrini
- Re: [AMBER] Fully random MPI error after updating CentOS from release 6.5 to 6.6 Jason Swails
- Re: [AMBER] NVT and NPT ensemble Jason Swails
- [AMBER] The question about REMD exchange ratio 王漠野
- Re: [AMBER] The question about REMD exchange ratio Jason Swails
- Re: [AMBER] NVT and NPT ensemble Sangita Kachhap
- Re: [AMBER] NVT and NPT ensemble Jason Swails
- Re: [AMBER] NVT and NPT ensemble Sangita Kachhap
- [AMBER] Strange behavior AMBER12 IBRAHIM M ABDELRADY
- Re: [AMBER] Strange behavior AMBER12 Adrian Roitberg
- Re: [AMBER] Strange behavior AMBER12 Jason Swails
- Re: [AMBER] Strange behavior AMBER12 IBRAHIM M ABDELRADY
- [AMBER] error message of addLJType of parmed: Action addLJType failed. UnhandledArgumentWarning: 0.0 0.0 sun
- Re: [AMBER] Strange behavior AMBER12 IBRAHIM M ABDELRADY
- Re: [AMBER] Fully random MPI error after updating CentOS from release 6.5 to 6.6 Massimiliano Porrini
- Re: [AMBER] error message of addLJType of parmed: Action addLJType failed. UnhandledArgumentWarning: 0.0 0.0 Jason Swails
- Re: [AMBER] Imaging Daniel Roe
- [AMBER] single dimension PMF calculation joan.montesdeoca.uns.edu.ar
- Re: [AMBER] error message of addLJType of parmed: Action addLJType failed. UnhandledArgumentWarning: 0.0 0.0 Ying-Chieh Sun
- [AMBER] aMD error maryam azimzadehirani
Tuesday, 4 November 2014
- [AMBER] Error logs James Starlight
- [AMBER] bug in pmemd softcore TI with SHAKE Hannes Loeffler
- Re: [AMBER] error message of addLJType of parmed: Action addLJType failed. UnhandledArgumentWarning: 0.0 0.0 Jason Swails
- Re: [AMBER] aMD error Jason Swails
Wednesday, 5 November 2014
- Re: [AMBER] aMD error maryam azimzadehirani
- [AMBER] AMBER Question: Setting box angle in tleap 曲薇
- Re: [AMBER] AMBER Question: Setting box angle in tleap David A Case
- [AMBER] AM1-BCC dipole moment CHAMI F.
- Re: [AMBER] AM1-BCC dipole moment David A Case
- Re: [AMBER] AM1-BCC dipole moment Jason Swails
- [AMBER] H-REMD Mele N.
- Re: [AMBER] H-REMD Carlos Simmerling
- Re: [AMBER] H-REMD Jason Swails
- Re: [AMBER] problem using pmemd.cuda with barostat=2 option Sorensen, Jesper
- Re: [AMBER] problem using pmemd.cuda with barostat=2 option Scott Le Grand
- Re: [AMBER] problem using pmemd.cuda with barostat=2 option Ross Walker
- Re: [AMBER] problem using pmemd.cuda with barostat=2 option Jason Swails
- Re: [AMBER] problem using pmemd.cuda with barostat=2 option Sorensen, Jesper
- [AMBER] NBCR AMBER Workshop - UCSD - Mon Dec 15th to Thur Dec 18th 2014 - Registration open. Ross Walker
Thursday, 6 November 2014
- [AMBER] cpptraj hist 3D CHAMI F.
- Re: [AMBER] cpptraj hist 3D Jason Swails
- Re: [AMBER] cpptraj hist 3D andrea spitaleri
- [AMBER] Binding energy using mm_pbsa.pl Wong, Sook (NIH/NCATS) [V]
- Re: [AMBER] cpptraj hist 3D Daniel Roe
- Re: [AMBER] cpptraj hist 3D andrea spitaleri
- [AMBER] determine free available space in simulation box Iqbal, Muhammad Sajid
- Re: [AMBER] cpptraj hist 3D Jason Swails
- Re: [AMBER] Binding energy using mm_pbsa.pl Aron Broom
- Re: [AMBER] cpptraj hist 3D andrea spitaleri
- Re: [AMBER] Binding energy using mm_pbsa.pl Wong, Sook (NIH/NCATS) [V]
- Re: [AMBER] Binding energy using mm_pbsa.pl Aron Broom
- Re: [AMBER] Binding energy using mm_pbsa.pl Jason Swails
- Re: [AMBER] Binding energy using mm_pbsa.pl Wong, Sook (NIH/NCATS) [V]
- Re: [AMBER] Binding energy using mm_pbsa.pl Jason Swails
- Re: [AMBER] Binding energy using mm_pbsa.pl Wong, Sook (NIH/NCATS) [V]
- Re: [AMBER] Binding energy using mm_pbsa.pl Aron Broom
- Re: [AMBER] Binding energy using mm_pbsa.pl Jason Swails
- [AMBER] Problems on PRMTOP file generation under ff02pol.r1 Wei Ye
- [AMBER] DRUG_PROTEIN INTERACTIOM Ruchika Bhat
- Re: [AMBER] DRUG_PROTEIN INTERACTIOM Wei Ye
Friday, 7 November 2014
- Re: [AMBER] DRUG_PROTEIN INTERACTIOM Ruchika Bhat
- [AMBER] bond distances in amber Mary Varughese
- [AMBER] hbonds Mary Varughese
- Re: [AMBER] DRUG_PROTEIN INTERACTIOM Wei Ye
- Re: [AMBER] DRUG_PROTEIN INTERACTIOM Jason Swails
- Re: [AMBER] bond distances in amber Jason Swails
- Re: [AMBER] hbonds Jason Swails
- [AMBER] Help needed regarding Ligand Protein MD studies Ruchika Bhat
- Re: [AMBER] Problems on PRMTOP file generation under ff02pol.r1 David A Case
- Re: [AMBER] Problems on PRMTOP file generation under ff02pol.r1 Wei Ye
- Re: [AMBER] Help needed regarding Ligand Protein MD studies Jason Swails
- Re: [AMBER] Help needed regarding Ligand Protein MD studies Wei Ye
- Re: [AMBER] Help needed regarding Ligand Protein MD studies Gulsevin,Alican
- Re: [AMBER] Help needed regarding Ligand Protein MD studies Ruchika Bhat
- Re: [AMBER] Help needed regarding Ligand Protein MD studies Wei Ye
- [AMBER] writing out restart files in netcdf format Sylvester Tumusiime
- Re: [AMBER] writing out restart files in netcdf format Christina Bergonzo
- Re: [AMBER] writing out restart files in netcdf format Sylvester Tumusiime
- Re: [AMBER] writing out restart files in netcdf format Christina Bergonzo
- Re: [AMBER] Help needed regarding Ligand Protein MD studies Ruchika Bhat
- Re: [AMBER] Help needed regarding Ligand Protein MD studies Ruchika Bhat
- Re: [AMBER] Binding energy using mm_pbsa.pl Wong, Sook (NIH/NCATS) [V]
Saturday, 8 November 2014
- Re: [AMBER] Help needed regarding Ligand Protein MD studies David A Case
- Re: [AMBER] Help needed regarding Ligand Protein MD studies Ruchika Bhat
- [AMBER] HEAT and PROD files for 10 ns run Ruchika Bhat
- Re: [AMBER] HEAT and PROD files for 10 ns run Jason Swails
- Re: [AMBER] bond distances in amber Mary Varughese
- Re: [AMBER] hbonds Mary Varughese
- [AMBER] simulation of peptide in alkane slab samarprit chakraborty
- Re: [AMBER] simulation of peptide in alkane slab nabil bennenni
- Re: [AMBER] bond distances in amber Niel Henriksen
- Re: [AMBER] bond distances in amber David A Case
- Re: [AMBER] Implicit simulation and MMPBSA/GBSA caculations Bajarang Kumbhar
Sunday, 9 November 2014
- Re: [AMBER] bond distances in amber Mary Varughese
- Re: [AMBER] simulation of peptide in alkane slab samarprit chakraborty
- Re: [AMBER] Implicit simulation and MMPBSA/GBSA caculations Jason Swails
- [AMBER] Which force field is "the best" Gonzalo Jimenez
- [AMBER] MMPBSA.py Sourav Purohit
- Re: [AMBER] Implicit simulation and MMPBSA/GBSA caculations Aron Broom
- [AMBER] Issue with DFTB-MD trajectory Perry, Jamin W.
- Re: [AMBER] Which force field is "the best" David A Case
- Re: [AMBER] MMPBSA.py Jason Swails
- [AMBER] Problems of pdb file convertion by pdb4amber and mmtsb LI An-Bang
Monday, 10 November 2014
- Re: [AMBER] Problems of pdb file convertion by pdb4amber and mmtsb David A Case
- Re: [AMBER] Which force field is "the best" Gonzalo Jimenez
- Re: [AMBER] Problems of pdb file convertion by pdb4amber and mmtsb Jason Swails
- [AMBER] a problem on heating the system ZHAO Ruisheng
- Re: [AMBER] a problem on heating the system Jason Swails
- Re: [AMBER] AM1-BCC dipole moment CHAMI F.
- Re: [AMBER] AM1-BCC dipole moment Jason Swails
- Re: [AMBER] a problem on heating the system David A Case
- Re: [AMBER] AM1-BCC dipole moment CHAMI F.
- Re: [AMBER] AM1-BCC dipole moment Hannes Loeffler
- [AMBER] Transition state John Smith
- [AMBER] Constant pH MD with CUDA not working BATUHAN KAV
- [AMBER] small molecules Lara rajam
- Re: [AMBER] small molecules David A Case
- [AMBER] Representing Sphere and Its parameterization in Amber. ATUL KUMAR
Tuesday, 11 November 2014
- Re: [AMBER] a problem on heating the system ZHAO Ruisheng
- Re: [AMBER] Representing Sphere and Its parameterization in Amber. David A Case
- Re: [AMBER] a problem on heating the system David A Case
- Re: [AMBER] Issue with DFTB-MD trajectory David A Case
- Re: [AMBER] a problem on heating the system ZHAO Ruisheng
- [AMBER] problem reimaging after strip WAT Pablo D. Dans Puiggròs
- Re: [AMBER] problem reimaging after strip WAT Jason Swails
- Re: [AMBER] problem reimaging after strip WAT Pablo D. Dans Puiggròs
- Re: [AMBER] problem reimaging after strip WAT Daniel Roe
- Re: [AMBER] problem reimaging after strip WAT Pablo D. Dans Puiggròs
- [AMBER] nativecontacts in ambertools14 Asmita Gupta
- Re: [AMBER] problem reimaging after strip WAT nabil bennenni
- [AMBER] cpptraj Sylvester Tumusiime
- Re: [AMBER] cpptraj Daniel Roe
- Re: [AMBER] nativecontacts in ambertools14 Daniel Roe
- Re: [AMBER] cpptraj nabil bennenni
- Re: [AMBER] cpptraj Sylvester Tumusiime
- Re: [AMBER] cpptraj Daniel Roe
- [AMBER] options "-ext" and "-pqr" of ambpdb are exlusive LI An-Bang
- Re: [AMBER] Representing Sphere and Its parameterization in Amber. ATUL KUMAR
Wednesday, 12 November 2014
- Re: [AMBER] a problem on heating the system David A Case
- Re: [AMBER] a problem on heating the system Jason Swails
- Re: [AMBER] options "-ext" and "-pqr" of ambpdb are exlusive Daniel Roe
- [AMBER] [Amber] Amber14 does not find parameters for Mg2+, please help Genin, Nicolas J
- Re: [AMBER] [Amber] Amber14 does not find parameters for Mg2+, please help Jason Swails
- [AMBER] time correlation function giulia palermo
- Re: [AMBER] time correlation function Daniel Roe
- Re: [AMBER] [Amber] Amber14 does not find parameters for Mg2+, please help Genin, Nicolas J
- [AMBER] Running explicit solvent CpHMD on GPUs Garrido Ruiz, Diego
- [AMBER] help Robin Jain
- [AMBER] The question about REMD exchange ratio 王漠野
- [AMBER] help in MD Robin Jain
Thursday, 13 November 2014
- [AMBER] Transition state Mahmood Jasim
- Re: [AMBER] The question about REMD exchange ratio Carlos Simmerling
- Re: [AMBER] help in MD Ayesha Fatima
- Re: [AMBER] time correlation function giulia palermo
- Re: [AMBER] help David A Case
- Re: [AMBER] Representing Sphere and Its parameterization in Amber. ATUL KUMAR
- Re: [AMBER] The question about REMD exchange ratio Jason Swails
- Re: [AMBER] Transition state Jason Swails
- Re: [AMBER] time correlation function Daniel Roe
- [AMBER] Calcium parameters in calmodulin bharat lakhani
- [AMBER] error in mmpbsa calculation Abdul wadood
- Re: [AMBER] Calcium parameters in calmodulin Jason Swails
- Re: [AMBER] error in mmpbsa calculation Jason Swails
- [AMBER] minimization problem Emilio Angelina
- Re: [AMBER] The question about REMD exchange ratio 王漠野
- [AMBER] Amber 14 installation problems 汪小涧
Friday, 14 November 2014
- Re: [AMBER] Amber 14 installation problems David A Case
- Re: [AMBER] minimization problem David A Case
- Re: [AMBER] options "-ext" and "-pqr" of ambpdb are exlusive David A Case
- Re: [AMBER] minimization problem Emilio Angelina
- Re: [AMBER] error in mmpbsa calculation Abdul wadood
- [AMBER] Entropy using Nmode Wong, Sook (NIH/NCATS) [V]
- [AMBER] Postdoctoral Position at the U.S. Army Research Laboratory in Coarse-Grain Modeling and Simulation Izvyekov, Sergiy (Sergey) CIV USARMY ARL (US)
- [AMBER] pmemd.MPI thermodynamic integration (TI) relative binding free energy set up psu4.uic.edu
- [AMBER] Is there a tool to calculate electron density maps averaged over a trajectory? Jose Borreguero
- Re: [AMBER] Is there a tool to calculate electron density maps averaged over a trajectory? David A Case
- Re: [AMBER] Entropy using Nmode Jason Swails
Saturday, 15 November 2014
- Re: [AMBER] pmemd.MPI thermodynamic integration (TI) relative binding free energy set up hannes.loeffler.stfc.ac.uk
- Re: [AMBER] GPU enabled Hardware specification M. Reza Ganjalikhany
- Re: [AMBER] Is there a tool to calculate electron density maps averaged over a trajectory? Jose Borreguero
- [AMBER] heme amber parameter Fatemeh Sadat Alavi
- [AMBER] Prmtop Sylvester Tumusiime
- Re: [AMBER] Prmtop Jason Swails
- Re: [AMBER] GPU enabled Hardware specification Ross Walker
- Re: [AMBER] heme amber parameter David A Case
- Re: [AMBER] GPU enabled Hardware specification M. Reza Ganjalikhany
Sunday, 16 November 2014
- [AMBER] Failure of antechamber with c -1 m 2 Francesco Pietra
- Re: [AMBER] GPU enabled Hardware specification Ross Walker
- Re: [AMBER] Failure of antechamber with c -1 m 2 David A Case
- Re: [AMBER] Failure of antechamber with c -1 m 2 Francesco Pietra
- Re: [AMBER] options "-ext" and "-pqr" of ambpdb are exlusive LI An-Bang
- [AMBER] MMPBSA.py nmode Sourav Purohit
- [AMBER] 4x GTX 980 Parker de Waal
- Re: [AMBER] 4x GTX 980 James Maier
- Re: [AMBER] 4x GTX 980 James Maier
- Re: [AMBER] Issue with DFTB-MD trajectory Perry, Jamin W.
Monday, 17 November 2014
- [AMBER] MMPBSA warning : No skew or curtosis when zero variance in moment Mina Madah
- Re: [AMBER] GPU enabled Hardware specification M. Reza Ganjalikhany
- Re: [AMBER] MMPBSA warning : No skew or curtosis when zero variance in moment Jason Swails
- Re: [AMBER] MMPBSA.py nmode Jason Swails
- [AMBER] Regarding pairdist function in cpptraj DEBOSTUTI GHOSHDASTIDAR
- Re: [AMBER] Regarding pairdist function in cpptraj Daniel Roe
- Re: [AMBER] Failure of antechamber with c -1 m 2 David A Case
- Re: [AMBER] Failure of antechamber with c -1 m 2 Francesco Pietra
- Re: [AMBER] help Robin Jain
- Re: [AMBER] help Jason Swails
- Re: [AMBER] GPU enabled Hardware specification Ross Walker
- [AMBER] MMPBSA.py normal mode analysis Sourav Purohit
- Re: [AMBER] MMPBSA.py normal mode analysis Jason Swails
- Re: [AMBER] MMPBSA.py normal mode analysis Sourav Purohit
- Re: [AMBER] GPU enabled Hardware specification M. Reza Ganjalikhany
- Re: [AMBER] 4x GTX 980 Scott Le Grand
- [AMBER] aMD on Amber 12 Aldo Segura
- Re: [AMBER] Regarding pairdist function in cpptraj DEBOSTUTI GHOSHDASTIDAR
- [AMBER] ERROR DURING "TESTING" OF AMBER INSTALLATION ROOPALI VERMA
Tuesday, 18 November 2014
- [AMBER] amber error about protein containing heme Fatemeh Sadat Alavi
- [AMBER] amber error about protein containing heme Fatemeh Sadat Alavi
- Re: [AMBER] ERROR DURING "TESTING" OF AMBER INSTALLATION David A Case
- Re: [AMBER] amber error about protein containing heme David A Case
- [AMBER] citation for mdout_analyser.py Krisztina Feher
- [AMBER] tleap not found in parallel amber14 Amihai
- Re: [AMBER] citation for mdout_analyser.py Jason Swails
- Re: [AMBER] tleap not found in parallel amber14 Jason Swails
- Re: [AMBER] amber error about protein containing heme Jason Swails
- Re: [AMBER] aMD on Amber 12 Daniel Roe
- Re: [AMBER] AMBER Digest, Vol 1041, Issue 1 Robin Jain
- Re: [AMBER] AMBER Digest, Vol 1041, Issue 1 Jason Swails
- Re: [AMBER] aMD on Amber 12 Aldo Segura
- Re: [AMBER] aMD on Amber 12 Daniel Roe
- [AMBER] nmr restraints and periodic boundary conditions Chris Moth
- Re: [AMBER] nmr restraints and periodic boundary conditions Jason Swails
- Re: [AMBER] nmr restraints and periodic boundary conditions Niel Henriksen
- Re: [AMBER] nmr restraints and periodic boundary conditions David A Case
- [AMBER] InputError when running MMBPSA.py HERBERT MAX VENTHUR PE¥A
- [AMBER] Is it possible to extract atomic charge information from the trajectory? Yip Yew Mun
- Re: [AMBER] ERROR DURING "TESTING" OF AMBER INSTALLATION ROOPALI VERMA
- Re: [AMBER] Is it possible to extract atomic charge information from the trajectory? Jason Swails
- Re: [AMBER] InputError when running MMBPSA.py Jason Swails
- [AMBER] Help generating Heme parameters 杨川
Wednesday, 19 November 2014
- Re: [AMBER] ERROR DURING "TESTING" OF AMBER INSTALLATION David A Case
- Re: [AMBER] ERROR DURING "TESTING" OF AMBER INSTALLATION Amihai
- [AMBER] box size changing during equilibration Robin Jain
- Re: [AMBER] box size changing during equilibration Daniel Roe
- [AMBER] Pairwise vs Sander with imin=5 kurisaki
- [AMBER] ERROR atom with mass 1 has type alreadydesignated as non-hydrogen type Abhishek TYAGI
- Re: [AMBER] Pairwise vs Sander with imin=5 Daniel Roe
- Re: [AMBER] Pairwise vs Sander with imin=5 kurisaki
- [AMBER] Error in CHAMBER output Abhishek TYAGI
- Re: [AMBER] Error in CHAMBER output Robin Betz
- Re: [AMBER] ERROR DURING "TESTING" OF AMBER INSTALLATION ROOPALI VERMA
- [AMBER] Reminder: NBCR AMBER Workshop - UCSD - Mon Dec 15th to Thur Dec 18th 2014 - Registration open. Ross Walker
Thursday, 20 November 2014
- [AMBER] adQM/MM vlimit exceeded problem Aixiao Li
- [AMBER] Problems with AmberTools test suite David A Case
- [AMBER] Errors compiling Amber 14 after applying update 7 Bob Healey
- Re: [AMBER] Pairwise vs Sander with imin=5 Daniel Roe
- [AMBER] PBSA error Kshatresh Dutta Dubey
- [AMBER] Can you use cholesterol lipid 11 parameters and lipid 14 lipid parameters? Jonathan Gough
- Re: [AMBER] Errors compiling Amber 14 after applying update 7 Jason Swails
- Re: [AMBER] PBSA error Jason Swails
- Re: [AMBER] PBSA error David A Case
- Re: [AMBER] Errors compiling Amber 14 after applying update 7 David A Case
- Re: [AMBER] Errors compiling Amber 14 after applying update 7 Ross Walker
- Re: [AMBER] PBSA error David A Case
- Re: [AMBER] PBSA error Kshatresh Dutta Dubey
- Re: [AMBER] PBSA error Kshatresh Dutta Dubey
- Re: [AMBER] PBSA error Ray Luo, Ph.D.
- [AMBER] MMPBSA.py bug with amber mask for stability/QH calculations Lawrenz, Morgan
- Re: [AMBER] MMPBSA.py bug with amber mask for stability/QH calculations Jason Swails
- [AMBER] The error when install amber12+AmberTools13 on Ubuntucd Biao Ma
- Re: [AMBER] The error when install amber12+AmberTools13 on Ubuntucd Jason Swails
- [AMBER] cut value in minimisation Robin Jain
- [AMBER] Bug Report Liu, Hui
Friday, 21 November 2014
- Re: [AMBER] cut value in minimisation Jason Swails
- Re: [AMBER] Bug Report Jason Swails
- [AMBER] cyclic peptide side chains Maria Diaz
- [AMBER] about nab m13654940810
- Re: [AMBER] cut value in minimisation David A Case
- Re: [AMBER] cyclic peptide side chains David A Case
- Re: [AMBER] about nab David A Case
- Re: [AMBER] Help generating Heme parameters Pengfei Li
- [AMBER] Issues with Cholesterol lipid11, lipid14 and lipid14_supp.lib Jonathan Gough
- [AMBER] Questions regarding GB simulations in Amber14 - ff14SBonlysc vs ff14SB - igb1 vs igb8 - hydrphobic force Marek Maly
- Re: [AMBER] Questions regarding GB simulations in Amber14 - ff14SBonlysc vs ff14SB - igb1 vs igb8 - hydrphobic force Carlos Simmerling
- [AMBER] Fwd: InputError when running MMBPSA.py HERBERT MAX VENTHUR PE¥A
- Re: [AMBER] Fwd: InputError when running MMBPSA.py Jason Swails
Saturday, 22 November 2014
- Re: [AMBER] amber error about protein containing heme Fatemeh Sadat Alavi
- Re: [AMBER] AMBER Digest, Vol 1045, Issue 1 Robin Jain
- Re: [AMBER] amber error about protein containing heme David A Case
- Re: [AMBER] AMBER Digest, Vol 1045, Issue 1 David A Case
- [AMBER] AMBER error: peek_ewald_inpcrd: SHOULD NOT BE HERE Hadeer ELHabashy
- Re: [AMBER] AMBER error: peek_ewald_inpcrd: SHOULD NOT BE HERE David A Case
- [AMBER] Installation error: recipe for target 'pupildata.o' failed Parker de Waal
- [AMBER] AMBER Unique atom types Brittany Boykin
- Re: [AMBER] Installation error: recipe for target 'pupildata.o' failed Parker de Waal
- Re: [AMBER] Installation error: recipe for target 'pupildata.o' failed David A Case
- Re: [AMBER] AMBER Unique atom types David A Case
- Re: [AMBER] Installation error: recipe for target 'pupildata.o' failed Parker de Waal
- Re: [AMBER] Installation error: recipe for target 'pupildata.o' failed Jason Swails
- Re: [AMBER] AMBER Unique atom types FyD
Sunday, 23 November 2014
- Re: [AMBER] Installation error: recipe for target 'pupildata.o' failed Parker de Waal
- Re: [AMBER] Installation error: recipe for target 'pupildata.o' failed Jason Swails
- Re: [AMBER] Installation error: recipe for target 'pupildata.o' failed Parker de Waal
- Re: [AMBER] 4x GTX 980 Parker de Waal
- [AMBER] How to seperate a protein-protein complex in PRMTOP and INPCRD files? LI An-Bang
- Re: [AMBER] 4x GTX 980 Scott Le Grand
- Re: [AMBER] 4x GTX 980 Scott Le Grand
- Re: [AMBER] 4x GTX 980 Parker de Waal
- Re: [AMBER] 4x GTX 980 Scott Le Grand
- Re: [AMBER] 4x GTX 980 Parker de Waal
- Re: [AMBER] 4x GTX 980 Scott Le Grand
- Re: [AMBER] Installation error: recipe for target 'pupildata.o' failed Jason Swails
- Re: [AMBER] How to seperate a protein-protein complex in PRMTOP and INPCRD files? Jason Swails
- Re: [AMBER] 4x GTX 980 Ross Walker
- Re: [AMBER] 4x GTX 980 Ross Walker
- Re: [AMBER] 4x GTX 980 Ross Walker
- Re: [AMBER] Installation error: recipe for target 'pupildata.o' failed Parker de Waal
- Re: [AMBER] Questions regarding GB simulations in Amber14 - ff14SBonlysc vs ff14SB - igb1 vs igb8 - hydrphobic force Marek Maly
- Re: [AMBER] adQM/MM vlimit exceeded problem Andreas Goetz
- Re: [AMBER] AMBER Digest, Vol 1044, Issue 1 Abhishek TYAGI
- [AMBER] errors in qm/mm Ayesha Fatima
- Re: [AMBER] errors in qm/mm Andreas Goetz
- Re: [AMBER] errors in qm/mm Ayesha Fatima
- Re: [AMBER] errors in qm/mm Ayesha Fatima
- [AMBER] Counseling about the GPU series supporting PMEMD geyushu.ustc.edu.cn
- Re: [AMBER] Counseling about the GPU series supporting PMEMD Ross Walker
Monday, 24 November 2014
- [AMBER] Glycan bond error leap maryam azimzadehirani
- Re: [AMBER] errors in qm/mm Marc van der Kamp
- Re: [AMBER] errors in qm/mm Ayesha Fatima
- Re: [AMBER] AMBER Digest, Vol 1044, Issue 1 Jason Swails
- Re: [AMBER] errors in qm/mm Gustavo Seabra
- Re: [AMBER] errors in qm/mm Ayesha Fatima
- Re: [AMBER] errors in qm/mm Gustavo Seabra
- Re: [AMBER] errors in qm/mm Ayesha Fatima
- [AMBER] Forcefield for DNA Baifan Wang
- Re: [AMBER] How to seperate a protein-protein complex in PRMTOP and INPCRD files? Daniel Roe
- [AMBER] Thermodynamic integration: Delta G of less soft core atoms is different from the one with more soft core atoms sun
- Re: [AMBER] Glycan bond error leap Jason Swails
- Re: [AMBER] Thermodynamic integration: Delta G of less soft core atoms is different from the one with more soft core atoms Hannes Loeffler
- Re: [AMBER] Glycan bond error leap Lachele Foley
- [AMBER] confirm b31b76c2dc0c4f0c33e4cac638252d6c6723f46d Zgarbova Marie
- Re: [AMBER] adQM/MM vlimit exceeded problem Andreas Goetz
- Re: [AMBER] Is there a tool to calculate electron density maps averaged over a trajectory? Pawel Janowski
- Re: [AMBER] The error when install amber12+AmberTools13 on Ubuntucd Biao Ma
- [AMBER] CHAMBER error Abhishek TYAGI
- Re: [AMBER] Glycan bond error leap maryam azimzadehirani
- [AMBER] doubt in RMD Mary Varughese
- [AMBER] hydophobicity Mary Varughese
Tuesday, 25 November 2014
- Re: [AMBER] Forcefield for DNA Petr Jurecka
- Re: [AMBER] Forcefield for DNA Baifan Wang
- [AMBER] Different PCA results when loading trajectories in a different order Guillaume Roellinger
- Re: [AMBER] Different PCA results when loading trajectories in a different order Daniel Roe
- Re: [AMBER] Different PCA results when loading trajectories in a different order Daniel Roe
- [AMBER] How to restrain atoms Akihiro Yamane
Wednesday, 26 November 2014
- Re: [AMBER] confirm b31b76c2dc0c4f0c33e4cac638252d6c6723f46d vojtech.mlynsky.upol.cz
- Re: [AMBER] Different PCA results when loading trajectories in a different order Guillaume Roellinger
- [AMBER] Free energy landscape anu chandra
- Re: [AMBER] How to restrain atoms David A Case
- Re: [AMBER] Different PCA results when loading trajectories in a different order Daniel Roe
- Re: [AMBER] Free energy landscape Daniel Roe
- Re: [AMBER] Free energy landscape Carlos Simmerling
- [AMBER] AmberTools13 Ibrahim Said
- [AMBER] GTX 780 Ti & GTX 980 Jordi Bujons
- Re: [AMBER] Different PCA results when loading trajectories in a different order Daniel Roe
- Re: [AMBER] AmberTools13 Daniel Roe
- Re: [AMBER] AmberTools13 Jason Swails
- Re: [AMBER] AmberTools13 David A Case
- Re: [AMBER] GTX 780 Ti & GTX 980 Ross Walker
- Re: [AMBER] doubt in RMD Jason Swails
- Re: [AMBER] hydophobicity Jason Swails
- Re: [AMBER] CHAMBER error Jason Swails
- Re: [AMBER] doubt in RMD Mary Varughese
- Re: [AMBER] hydophobicity Mary Varughese
Thursday, 27 November 2014
- [AMBER] Fw: Elham tazikeh
- [AMBER] Amber 14 and NetCDF installation issue Fernando Ezequiel Chain
- Re: [AMBER] AmberTools13 Ibrahim Said
- Re: [AMBER] hydophobicity Jason Swails
- Re: [AMBER] Free energy landscape anu chandra
- Re: [AMBER] doubt in RMD Jason Swails
- Re: [AMBER] (no subject) Jason Swails
- Re: [AMBER] Amber 14 and NetCDF installation issue Jason Swails
- Re: [AMBER] AmberTools13 Jason Swails
- [AMBER] xLEaP Na+ Cl- Weinzierl, Robert O J
- Re: [AMBER] xLEaP Na+ Cl- Asaminew Haile
- Re: [AMBER] doubt in RMD Mary Varughese
- Re: [AMBER] hydophobicity Mary Varughese
- [AMBER] Interaction energy between two dimer unit Soumendranath Bhakat
Friday, 28 November 2014
- Re: [AMBER] How to restrain atoms Akihiro Yamane
- [AMBER] installing amber12 in GPU Vijay Achari
- [AMBER] minimization question Carlos Romero
- Re: [AMBER] minimization question David A Case
- [AMBER] Correct script for B-factor Soumendranath Bhakat
- Re: [AMBER] minimization question Carlos Romero
- Re: [AMBER] Correct script for B-factor Marcus Arieno
- [AMBER] QM/MM adaptive biased MD_ABMD Aixiao Li
- Re: [AMBER] Correct script for B-factor David A Case
- Re: [AMBER] QM/MM adaptive biased MD_ABMD David A Case
- Re: [AMBER] QM/MM adaptive biased MD_ABMD Aixiao Li
- Re: [AMBER] installing amber12 in GPU Jason Swails
- [AMBER] generate topology file and parameter file for complex with dummy atoms Jorgen Simonsen
- Re: [AMBER] generate topology file and parameter file for complex with dummy atoms Jason Swails
- Re: [AMBER] Interaction energy between two dimer unit Jason Swails
- [AMBER] Calcium vdW parameters Caitlin Scott
- Re: [AMBER] Calcium vdW parameters mmaestre.gate.sinica.edu.tw
- Re: [AMBER] doubt in RMD Jason Swails
- Re: [AMBER] Correct script for B-factor Soumendranath Bhakat
- [AMBER] Metal parameterization sailu
- [AMBER] Monitoring pi-cationic interaction asdda asa
Saturday, 29 November 2014
- Re: [AMBER] doubt in RMD Mary Varughese
- Re: [AMBER] Calcium vdW parameters Ken Merz
- Re: [AMBER] Metal parameterization Ken Merz
- Re: [AMBER] generate topology file and parameter file for complex with dummy atoms Jorgen Simonsen
Sunday, 30 November 2014
- [AMBER] PARALLEL INSTALLATION ERROR Nalini Chauhan
- Re: [AMBER] PARALLEL INSTALLATION ERROR Jason Swails
- [AMBER] 100ps long minimization script pradeep pant
- Re: [AMBER] 100ps long minimization script Carlos Simmerling
- [AMBER] Problem with triangular point in parameter file Jorgen Simonsen
- Re: [AMBER] Correct script for B-factor Daniel Roe
- Re: [AMBER] hydophobicity Daniel Roe
- Re: [AMBER] Monitoring pi-cationic interaction Daniel Roe
- Re: [AMBER] 100ps long minimization script David A Case
- Re: [AMBER] Problem with triangular point in parameter file David A Case
- Re: [AMBER] Problem with triangular point in parameter file Jorgen Simonsen

Last message date: Sun Nov 30 2014 - 15:00:02 PST
Archived on: Mon Feb 03 2025 - 05:54:58 PST

Amber Archive Nov 2014 by date