Amber Archive Jan 2018 by author
334 messages
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Starting
Mon Jan 01 2018 - 23:00:02 PST,
Ending
Wed Jan 31 2018 - 10:00:02 PST
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Aashish Bhatt
Re: [AMBER] Regarding error in preparation of HEME via MCPB.py
(Thu Jan 25 2018 - 22:47:02 PST)
Re: [AMBER] Regarding error in preparation of HEME via MCPB.py
(Mon Jan 22 2018 - 03:33:43 PST)
[AMBER] Regarding error in preparation of HEME via MCPB.py
(Mon Jan 08 2018 - 20:47:34 PST)
Abdul-Rashid III Sampaco
[AMBER] pseudo-trajectory in pytraj
(Wed Jan 10 2018 - 09:04:17 PST)
ABEL Stephane
Re: [AMBER] Is there anyway to recover the potential energies obtained after running md
(Wed Jan 31 2018 - 09:23:57 PST)
Re: [AMBER] Empty .frcmod file
(Tue Jan 30 2018 - 09:36:02 PST)
Re: [AMBER] Empty .frcmod file
(Tue Jan 30 2018 - 07:38:51 PST)
Re: [AMBER] Empty .frcmod file
(Tue Jan 30 2018 - 06:34:45 PST)
Re: [AMBER] Empty .frcmod file
(Tue Jan 30 2018 - 06:31:39 PST)
Re: [AMBER] RESP charges for capped C termimal glycine: NHCH2CONH2
(Sun Jan 14 2018 - 04:02:05 PST)
[AMBER] RESP charges for capped C termimal glycine: NHCH2CONH2
(Sat Jan 13 2018 - 05:50:17 PST)
Ahmed Mashaly
[AMBER] Acpype and Gromacs
(Wed Jan 24 2018 - 12:42:11 PST)
Re: [AMBER] Reorienting the protein during simulation
(Fri Jan 19 2018 - 08:25:22 PST)
Re: [AMBER] Reorienting the protein during simulation
(Wed Jan 17 2018 - 02:39:01 PST)
[AMBER] Reorienting the protein during simulation
(Tue Jan 16 2018 - 02:52:20 PST)
Alan
Re: [AMBER] Acpype and Gromacs
(Thu Jan 25 2018 - 00:57:16 PST)
Alberto Bencomo
Re: [AMBER] Is there anyway to recover the potential energies obtained after running md
(Wed Jan 31 2018 - 08:39:44 PST)
[AMBER] Problem to convert
(Thu Jan 25 2018 - 08:23:31 PST)
Alessandro Contini
Re: [AMBER] Parametrization of new amino acid in methanol solvent
(Fri Jan 19 2018 - 05:03:50 PST)
Amen Shamim
[AMBER] Protonated cytosine and adenine: Parameter file was not saved
(Thu Jan 25 2018 - 05:15:28 PST)
Andreas Tosstorff
Re: [AMBER] umbrella sampling process
(Wed Jan 17 2018 - 10:22:50 PST)
[AMBER] REMD job stops on loadleveler
(Mon Jan 08 2018 - 11:56:21 PST)
Angela dos Reis
[AMBER] Amber mailing list
(Fri Jan 12 2018 - 17:54:16 PST)
Antonija Tomić
Re: [AMBER] scaling of electrostatic interactions
(Thu Jan 11 2018 - 02:49:12 PST)
[AMBER] scaling of electrostatic interactions
(Thu Jan 11 2018 - 02:18:00 PST)
anu chandra
Re: [AMBER] Distance calculation between atoms from two different frames using CPPTRAJ
(Fri Jan 05 2018 - 02:35:32 PST)
[AMBER] Distance calculation between atoms from two different frames using CPPTRAJ
(Thu Jan 04 2018 - 03:41:56 PST)
Arati Paudyal
Re: [AMBER] CPPTRAJ-Angle between two Helices
(Fri Jan 19 2018 - 13:15:42 PST)
Audrius Laurynėnas
[AMBER] Unreplicable AMBER tutorial 3
(Tue Jan 23 2018 - 04:22:21 PST)
Bakary N'tji Diallo
Re: [AMBER] Ligand modifying softwares.
(Fri Jan 19 2018 - 01:21:54 PST)
Batuhan Kav
Re: [AMBER] Cannot match namelist object name 0
(Wed Jan 24 2018 - 09:52:34 PST)
Re: [AMBER] Writing mdcrd to inpcrd
(Mon Jan 22 2018 - 05:20:44 PST)
Bhargava Sai M
Re: [AMBER] Errors in my installation
(Wed Jan 17 2018 - 21:29:09 PST)
[AMBER] Errors in my installation
(Tue Jan 16 2018 - 20:52:23 PST)
Bill Ross
[AMBER] going away for now
(Fri Jan 12 2018 - 18:26:01 PST)
Re: [AMBER] Problem regarding compiling in cpptraj with openmp
(Thu Jan 04 2018 - 23:58:52 PST)
Re: [AMBER] Problem regarding compiling in cpptraj with openmp
(Thu Jan 04 2018 - 23:05:53 PST)
Re: [AMBER] Problem regarding compiling in cpptraj with openmp
(Thu Jan 04 2018 - 22:58:35 PST)
Carlos Simmerling
Re: [AMBER] Is there anyway to recover the potential energies obtained after running md
(Wed Jan 31 2018 - 08:36:23 PST)
Re: [AMBER] Query regarding the ff99SB*ildn force field
(Wed Jan 31 2018 - 06:01:54 PST)
Re: [AMBER] GBSA parameters
(Sun Jan 28 2018 - 13:27:17 PST)
Re: [AMBER] GBSA parameters
(Sun Jan 28 2018 - 06:59:49 PST)
Celeste Sagui
Re: [AMBER] Metadynamics in pmemd
(Thu Jan 25 2018 - 14:51:20 PST)
Chetna Tyagi
[AMBER] Parametrization of new amino acid in methanol solvent
(Fri Jan 19 2018 - 04:10:51 PST)
Chris Neale
[AMBER] Can amber16 pmemd rigorously combine position restraints with pressure coupling on GPUs ?
(Fri Jan 26 2018 - 11:48:09 PST)
Re: [AMBER] Amber 16.12 and 12-6-4 force field Problem
(Sat Jan 13 2018 - 19:01:44 PST)
Cruzeiro,Vinicius Wilian D
Re: [AMBER] constant pH md
(Thu Jan 11 2018 - 04:04:06 PST)
Crystal Vander Zanden
[AMBER] Best practices for lipid equilibration - Amber parameters in Gromacs
(Mon Jan 22 2018 - 08:13:30 PST)
[AMBER] Trying to use AMBER parameters in GROMACS
(Wed Jan 03 2018 - 08:49:35 PST)
Daniel Mermelstein
Re: [AMBER] Binding energy of ligand with homology model
(Wed Jan 03 2018 - 13:31:50 PST)
Daniel Roe
Re: [AMBER] cpptraj long writing queue
(Wed Jan 24 2018 - 03:10:58 PST)
Re: [AMBER] fatty acid ligand comes out of binding site during md.
(Tue Jan 23 2018 - 08:36:47 PST)
Re: [AMBER] CPPTRAJ-Angle between two Helices
(Fri Jan 19 2018 - 14:39:24 PST)
Re: [AMBER] Installation - NetCDF C compile failed
(Fri Jan 19 2018 - 12:30:06 PST)
Re: [AMBER] CPPTRAJ-Angle between two Helices
(Fri Jan 19 2018 - 12:24:10 PST)
Re: [AMBER] Installation - NetCDF C compile failed
(Fri Jan 19 2018 - 11:35:03 PST)
Re: [AMBER] Mail from "Dr. MANAS MONDAL" <manas.pku.edu.cn>.
(Fri Jan 19 2018 - 05:31:13 PST)
Re: [AMBER] Reorienting the protein during simulation
(Wed Jan 17 2018 - 07:55:13 PST)
Re: [AMBER] more than 100% hydrogen bond population
(Tue Jan 16 2018 - 06:57:32 PST)
Re: [AMBER] Reorienting the protein during simulation
(Tue Jan 16 2018 - 06:54:33 PST)
Re: [AMBER] distance to center of geometry
(Tue Jan 16 2018 - 06:46:05 PST)
Re: [AMBER] constant pH md
(Tue Jan 16 2018 - 06:44:08 PST)
Re: [AMBER] H-bond analysis in tetrameric protein complexes
(Tue Jan 16 2018 - 06:42:37 PST)
Re: [AMBER] Fwd: Hydrophobic interaction VS time in protein interfaces
(Tue Jan 16 2018 - 06:41:52 PST)
Re: [AMBER] gnuplot x-axis represented the number of frames how to convert it in nano second time.
(Wed Jan 10 2018 - 07:00:13 PST)
Re: [AMBER] cpptraj.OMP vs cpptraj
(Wed Jan 10 2018 - 06:20:43 PST)
Re: [AMBER] gnuplot x-axis represented the number of frames how to convert it in nano second time.
(Wed Jan 10 2018 - 06:13:52 PST)
Re: [AMBER] Which command to use for printing X Y Z coordinates of the given atom ?
(Fri Jan 05 2018 - 06:02:50 PST)
Re: [AMBER] Problem regarding compiling in cpptraj with openmp
(Fri Jan 05 2018 - 05:37:47 PST)
Re: [AMBER] Distance calculation between atoms from two different frames using CPPTRAJ
(Thu Jan 04 2018 - 06:00:38 PST)
Re: [AMBER] CPPTRAJ HBOND
(Tue Jan 02 2018 - 10:21:00 PST)
Re: [AMBER] DSSP CPPtraj
(Tue Jan 02 2018 - 10:12:51 PST)
daniele selli
[AMBER] AMBER - QMMM with DFTB
(Thu Jan 18 2018 - 01:59:50 PST)
Darrin York
Re: [AMBER] AMBER GPU-TI implementation - paper?
(Thu Jan 11 2018 - 06:46:03 PST)
Re: [AMBER] AMBER GPU-TI implementation - paper?
(Thu Jan 11 2018 - 06:16:02 PST)
David A Case
Re: [AMBER] Query regarding the ff99SB*ildn force field
(Wed Jan 31 2018 - 05:32:55 PST)
Re: [AMBER] Use amber output velocity for different system
(Mon Jan 29 2018 - 11:57:58 PST)
Re: [AMBER] EVB xch_* values
(Mon Jan 29 2018 - 09:14:51 PST)
Re: [AMBER] Amber16+AT17: Several checks failing w/Intel Parallel Studio XE 2018.1
(Mon Jan 29 2018 - 09:10:39 PST)
Re: [AMBER] Metadynamics in pmemd
(Mon Jan 29 2018 - 09:01:42 PST)
Re: [AMBER] Can amber16 pmemd rigorously combine position restraints with pressure coupling on GPUs ?
(Mon Jan 29 2018 - 08:45:36 PST)
Re: [AMBER] command not working
(Mon Jan 29 2018 - 05:12:58 PST)
Re: [AMBER] command problem
(Mon Jan 29 2018 - 05:09:44 PST)
Re: [AMBER] box size and SMD simulation
(Sun Jan 28 2018 - 18:44:47 PST)
Re: [AMBER] GBSA parameters
(Sun Jan 28 2018 - 18:32:21 PST)
Re: [AMBER] Compressing trajectory file
(Fri Jan 26 2018 - 18:09:34 PST)
Re: [AMBER] Problem to convert
(Fri Jan 26 2018 - 04:51:31 PST)
Re: [AMBER] Protonated cytosine and adenine: Parameter file was not saved
(Thu Jan 25 2018 - 06:52:16 PST)
Re: [AMBER] Non-PBC simulation in a droplet made of organic solvent
(Tue Jan 23 2018 - 12:38:12 PST)
Re: [AMBER] Avoiding pdb4amber renumbering
(Tue Jan 23 2018 - 12:14:22 PST)
Re: [AMBER] How to perform Newton-Raphson minimization to protein
(Tue Jan 23 2018 - 05:26:46 PST)
Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber
(Mon Jan 22 2018 - 18:44:45 PST)
Re: [AMBER] PROBLEM ENCOUNTERED WHILE UNDERGOING TUTUORIAL FOR ROOM TEMPERATURE IONIC LIQUID.
(Mon Jan 22 2018 - 05:33:32 PST)
Re: [AMBER] Writing mdcrd to inpcrd
(Mon Jan 22 2018 - 05:31:02 PST)
Re: [AMBER] Installation - NetCDF C compile failed
(Sat Jan 20 2018 - 14:41:41 PST)
Re: [AMBER] Installation - NetCDF C compile failed
(Sat Jan 20 2018 - 07:29:35 PST)
Re: [AMBER] Amber 18
(Fri Jan 19 2018 - 06:55:56 PST)
Re: [AMBER] Crystal water in Amber 16
(Thu Jan 18 2018 - 05:23:47 PST)
Re: [AMBER] AMBER tools 17 installation problem
(Wed Jan 17 2018 - 15:52:33 PST)
Re: [AMBER] RESP charges for capped C termimal glycine: NHCH2CONH2
(Sun Jan 14 2018 - 06:01:30 PST)
Re: [AMBER] Amber mailing list
(Sat Jan 13 2018 - 06:01:31 PST)
Re: [AMBER] error 12-6-4 LJ with the last update (November 2017)
(Thu Jan 11 2018 - 04:52:39 PST)
Re: [AMBER] MMGBSA calculation gives very high positive free energy of binding!!!
(Thu Jan 11 2018 - 04:38:49 PST)
Re: [AMBER] OS High Sierra
(Thu Jan 11 2018 - 04:32:41 PST)
Re: [AMBER] prmtop.pdf %FLAG SCREEN
(Wed Jan 10 2018 - 10:53:08 PST)
Re: [AMBER] use_template = 0
(Wed Jan 10 2018 - 08:43:19 PST)
Re: [AMBER] ligand outside the binding site - vmd visualisation problem
(Wed Jan 10 2018 - 05:19:08 PST)
Re: [AMBER] REMD job stops on loadleveler
(Tue Jan 09 2018 - 08:23:42 PST)
Re: [AMBER] Minimization Problem(error shows "... RESTARTED DUE TO LINMIN FAILURE ..." )
(Sun Jan 07 2018 - 17:41:19 PST)
Re: [AMBER] Minimization Problem(error shows "... RESTARTED DUE TO LINMIN FAILURE ..." )
(Sun Jan 07 2018 - 05:37:14 PST)
Re: [AMBER] qm2_extern_gau_module
(Fri Jan 05 2018 - 12:04:18 PST)
David Cerutti
Re: [AMBER] Transformation from cartesian to torsion space
(Mon Jan 22 2018 - 13:39:50 PST)
Re: [AMBER] distance to center of geometry
(Mon Jan 15 2018 - 21:31:05 PST)
Re: [AMBER] RESP charges for capped C termimal glycine: NHCH2CONH2
(Sat Jan 13 2018 - 20:33:57 PST)
Re: [AMBER] Amber 16.12 and 12-6-4 force field Problem
(Thu Jan 11 2018 - 21:11:55 PST)
Re: [AMBER] error 12-6-4 LJ with the last update (November 2017)
(Thu Jan 11 2018 - 10:55:34 PST)
David Poole
Re: [AMBER] qm2_extern_gau_module
(Sat Jan 06 2018 - 14:48:40 PST)
Re: [AMBER] qm2_extern_gau_module
(Sat Jan 06 2018 - 14:42:09 PST)
David Sáez
Re: [AMBER] About rerun the same trajectory
(Wed Jan 31 2018 - 09:40:32 PST)
Re: [AMBER] About rerun the same trajectory
(Wed Jan 31 2018 - 07:49:42 PST)
[AMBER] About rerun the same trajectory
(Wed Jan 31 2018 - 07:20:54 PST)
Re: [AMBER] dftb_chg not working
(Mon Jan 29 2018 - 04:18:53 PST)
[AMBER] dftb_chg not working
(Mon Jan 29 2018 - 03:54:55 PST)
[AMBER] Change a residue in a protein
(Thu Jan 18 2018 - 00:45:47 PST)
Davide Sala
Re: [AMBER] error 12-6-4 LJ with the last update (November 2017)
(Thu Jan 11 2018 - 05:49:23 PST)
[AMBER] error 12-6-4 LJ with the last update (November 2017)
(Thu Jan 11 2018 - 02:53:31 PST)
Dr. MANAS MONDAL
[AMBER] Mail from "Dr. MANAS MONDAL" <manas.pku.edu.cn>.
(Fri Jan 19 2018 - 01:48:01 PST)
Elvis Martis
Re: [AMBER] Empty .frcmod file
(Tue Jan 30 2018 - 06:30:53 PST)
Re: [AMBER] Empty .frcmod file
(Tue Jan 30 2018 - 05:51:43 PST)
Re: [AMBER] Compressing trajectory file
(Fri Jan 26 2018 - 05:56:25 PST)
Fabian Glaser
[AMBER] AMBER workshop registration opened, 4-8 March, Technion, Israel
(Wed Jan 10 2018 - 00:07:14 PST)
[AMBER] Announcement: AMBER Molecular Dynamics Workshop 2018
(Sun Jan 07 2018 - 06:37:11 PST)
Goetz, Andreas
Re: [AMBER] QM/MM SMD with 'external' theory and PBCs
(Fri Jan 26 2018 - 15:20:53 PST)
Re: [AMBER] QM/MM metadynamics with external QM code
(Fri Jan 26 2018 - 02:20:18 PST)
Re: [AMBER] AMBER - QMMM with DFTB
(Thu Jan 18 2018 - 11:29:21 PST)
Re: [AMBER] QM/MM MD B3LYP
(Wed Jan 10 2018 - 21:00:20 PST)
Re: [AMBER] qm2_extern_gau_module
(Fri Jan 05 2018 - 13:37:55 PST)
Guanglin Kuang
Re: [AMBER] Amber 16.12 and 12-6-4 force field Problem
(Thu Jan 11 2018 - 22:01:56 PST)
[AMBER] Amber 16.12 and 12-6-4 force field Problem
(Thu Jan 11 2018 - 18:49:22 PST)
Gustavo Seabra
Re: [AMBER] AMBER - QMMM with DFTB
(Thu Jan 18 2018 - 05:22:47 PST)
Hadházi Ádám
Re: [AMBER] AMBER GPU-TI implementation - paper?
(Thu Jan 11 2018 - 06:26:51 PST)
[AMBER] AMBER GPU-TI implementation - paper?
(Thu Jan 11 2018 - 05:37:07 PST)
Hai Nguyen
Re: [AMBER] GBSA parameters
(Sun Jan 28 2018 - 17:26:34 PST)
Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber
(Fri Jan 26 2018 - 11:09:42 PST)
Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber
(Tue Jan 23 2018 - 19:30:35 PST)
Re: [AMBER] Avoiding pdb4amber renumbering
(Tue Jan 23 2018 - 11:11:42 PST)
Re: [AMBER] Installation - NetCDF C compile failed
(Sat Jan 20 2018 - 15:39:06 PST)
Re: [AMBER] Installation - NetCDF C compile failed
(Fri Jan 19 2018 - 10:25:13 PST)
Re: [AMBER] Crystal water in Amber 16
(Wed Jan 17 2018 - 22:05:47 PST)
Re: [AMBER] Errors in my installation
(Wed Jan 17 2018 - 14:38:08 PST)
Re: [AMBER] AMBER tools 17 installation problem
(Wed Jan 17 2018 - 14:36:02 PST)
Re: [AMBER] pseudo-trajectory in pytraj
(Wed Jan 10 2018 - 09:54:33 PST)
Re: [AMBER] Which command to use for printing X Y Z coordinates of the given atom ?
(Thu Jan 04 2018 - 19:09:03 PST)
Hallel Freedman
Re: [AMBER] OS High Sierra
(Fri Jan 26 2018 - 07:32:39 PST)
[AMBER] OS High Sierra
(Wed Jan 10 2018 - 16:36:51 PST)
Hannes Konegger
[AMBER] Metadynamics in pmemd
(Thu Jan 25 2018 - 05:13:39 PST)
Ibrahim Said
[AMBER] box size and SMD simulation
(Sun Jan 28 2018 - 10:18:46 PST)
Jacopo Sgrignani
Re: [AMBER] QM/MM metadynamics with external QM code
(Fri Jan 26 2018 - 03:26:44 PST)
Jag Silwal
Re: [AMBER] CPPTRAJ-Angle between two Helices
(Fri Jan 19 2018 - 13:17:03 PST)
[AMBER] CPPTRAJ-Angle between two Helices
(Fri Jan 19 2018 - 10:23:06 PST)
[AMBER] H-bond analysis in tetrameric protein complexes
(Mon Jan 15 2018 - 13:09:44 PST)
Re: [AMBER] Fwd: Hydrophobic interaction VS time in protein interfaces
(Sun Jan 14 2018 - 09:06:44 PST)
[AMBER] Hydrophobic interaction VS time in protein interfaces
(Tue Jan 09 2018 - 08:45:38 PST)
Jason Swails
Re: [AMBER] MMGBSA calculations with explicit water molecules
(Sat Jan 20 2018 - 18:06:23 PST)
Re: [AMBER] Amber 16.12 and 12-6-4 force field Problem
(Thu Jan 18 2018 - 19:14:06 PST)
Re: [AMBER] AmberTools with Amber11
(Thu Jan 18 2018 - 18:58:47 PST)
Re: [AMBER] Replica exchange thermodynamic integration in AMBER
(Thu Jan 18 2018 - 10:51:15 PST)
Re: [AMBER] error 12-6-4 LJ with the last update (November 2017)
(Thu Jan 18 2018 - 10:49:44 PST)
Re: [AMBER] constant pH md
(Tue Jan 16 2018 - 06:59:52 PST)
Re: [AMBER] constant pH md
(Mon Jan 15 2018 - 18:33:10 PST)
Re: [AMBER] Trying to use AMBER parameters in GROMACS
(Fri Jan 05 2018 - 21:18:37 PST)
Re: [AMBER] Trying to use AMBER parameters in GROMACS
(Fri Jan 05 2018 - 21:18:04 PST)
Jennifer L. Muzyka
[AMBER] AmberTools with Amber11
(Thu Jan 18 2018 - 11:35:22 PST)
Jeyaram R A
Re: [AMBER] Writing mdcrd to inpcrd
(Mon Jan 22 2018 - 08:32:08 PST)
[AMBER] error during MMPBSA-reg
(Fri Jan 19 2018 - 06:47:34 PST)
[AMBER] Error during MMPBSA calculation -reg.
(Wed Jan 17 2018 - 03:40:01 PST)
Re: [AMBER] MD run saving only 250 frames
(Tue Jan 16 2018 - 23:14:29 PST)
[AMBER] error during MMPBSA calculation -reg.
(Wed Jan 10 2018 - 23:06:16 PST)
[AMBER] Error during the MMPBSA calculation -reg.
(Mon Jan 08 2018 - 20:34:04 PST)
Jiří Dluhoš
Re: [AMBER] Installation - NetCDF C compile failed
(Sat Jan 20 2018 - 14:15:12 PST)
Re: [AMBER] Installation - NetCDF C compile failed
(Fri Jan 19 2018 - 12:13:19 PST)
Re: [AMBER] Installation - NetCDF C compile failed
(Fri Jan 19 2018 - 10:35:27 PST)
[AMBER] Installation - NetCDF C compile failed
(Fri Jan 19 2018 - 10:23:31 PST)
Johannes Kalliauer
[AMBER] prmtop.pdf %FLAG SCREEN
(Tue Jan 09 2018 - 04:53:21 PST)
Jonas Mansoor
[AMBER] Compiling AMBER16 with Open MPI 3.x
(Wed Jan 31 2018 - 01:15:09 PST)
Kellon Belfon
Re: [AMBER] parmchk
(Sat Jan 27 2018 - 22:37:40 PST)
Kenneth Huang
[AMBER] hbond analysis on DNA-protein complex
(Mon Jan 29 2018 - 07:26:47 PST)
Kenneth McGuinness
[AMBER] Patent to solve floating point errors
(Thu Jan 18 2018 - 14:41:33 PST)
Khabiri, Morteza
[AMBER] Use amber output velocity for different system
(Mon Jan 29 2018 - 08:48:11 PST)
khair.bux.iccs.edu
[AMBER] email
(Tue Jan 16 2018 - 01:58:45 PST)
krishna.2015.iitg.ernet.in
[AMBER] umbrella sampling process
(Wed Jan 17 2018 - 10:04:33 PST)
Lara rajam
[AMBER] leap
(Tue Jan 16 2018 - 09:26:39 PST)
Leena Aggarwal
[AMBER] Query regarding the ff99SB*ildn force field
(Tue Jan 30 2018 - 20:53:26 PST)
Lorenzo Gontrani
Re: [AMBER] scaling of electrostatic interactions
(Thu Jan 11 2018 - 02:19:49 PST)
Luka Bilić
Re: [AMBER] Ligand modifying softwares.
(Fri Jan 19 2018 - 01:28:01 PST)
M. Pyrka
[AMBER] ligand outside the binding site - vmd visualisation problem
(Wed Jan 10 2018 - 03:47:50 PST)
Maciej Maciejczyk
Re: [AMBER] constant pH md
(Thu Jan 11 2018 - 04:52:16 PST)
[AMBER] constant pH md
(Wed Jan 10 2018 - 23:44:21 PST)
Mahendra B Thapa
[AMBER] resources for summer researches
(Mon Jan 08 2018 - 10:35:33 PST)
Malay Raul
Re: [AMBER] Minimization Problem(error shows "... RESTARTED DUE TO LINMIN FAILURE ..." )
(Sun Jan 07 2018 - 12:28:38 PST)
[AMBER] Minimization Problem(error shows "... RESTARTED DUE TO LINMIN FAILURE ..." )
(Sat Jan 06 2018 - 13:05:13 PST)
Marawan Hussien
[AMBER] MMGBSA calculations with explicit water molecules
(Thu Jan 18 2018 - 12:14:15 PST)
Marcelo Andrade Chagas
Re: [AMBER] QM/MM MD B3LYP
(Wed Jan 10 2018 - 09:43:58 PST)
Marek Maly
[AMBER] Which command to use for printing X Y Z coordinates of the given atom ?
(Thu Jan 04 2018 - 17:54:07 PST)
Re: [AMBER] LIPID17 reference ?
(Wed Jan 03 2018 - 07:32:39 PST)
[AMBER] LIPID17 reference ?
(Wed Jan 03 2018 - 05:37:01 PST)
Marie Brut
[AMBER] DNA melting temperature
(Tue Jan 09 2018 - 01:16:13 PST)
Markowska
Re: [AMBER] PROBLEM ENCOUNTERED WHILE UNDERGOING TUTUORIAL FOR ROOM TEMPERATURE IONIC LIQUID.
(Mon Jan 22 2018 - 05:55:55 PST)
maryam azimzadehirani
[AMBER] AMBER tools 17 installation problem
(Wed Jan 17 2018 - 08:20:45 PST)
matheus froeyen
Re: [AMBER] DNA melting temperature
(Tue Jan 09 2018 - 02:56:32 PST)
Meng Wu
[AMBER] distance to center of geometry
(Mon Jan 15 2018 - 19:27:06 PST)
Mohd Farid Ismail
[AMBER] Extract Velocity (and Force) from Gromacs .trr trajectory using cpptraj
(Thu Jan 25 2018 - 02:19:19 PST)
MOHD HOMAIDUR RAHMAN
Re: [AMBER] xmgr x-axis change to ns.
(Sun Jan 07 2018 - 01:26:07 PST)
Morrow,John Kenneth
Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB 3C
(Sat Jan 27 2018 - 06:03:46 PST)
[AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB 3C
(Fri Jan 19 2018 - 15:14:12 PST)
Muthukumaran Rajagopalan
[AMBER] Query on thermodynamic integration of complexes involving metal ions
(Wed Jan 31 2018 - 05:16:02 PST)
[AMBER] Query on thermodynamic integration of complexes involving metal ions
(Wed Jan 31 2018 - 04:24:55 PST)
Nikolay N. Kuzmich
[AMBER] Atom restraints in AMBER
(Tue Jan 09 2018 - 18:33:02 PST)
Núbia Prates
Re: [AMBER] Cannot match namelist object name 0
(Thu Jan 25 2018 - 05:23:02 PST)
[AMBER] Cannot match namelist object name 0
(Wed Jan 24 2018 - 08:26:33 PST)
Patrice Peterson
Re: [AMBER] Amber16+AT17: Several checks failing w/Intel Parallel Studio XE 2018.1
(Tue Jan 23 2018 - 12:55:00 PST)
Re: [AMBER] Amber16+AT17: Several checks failing w/Intel Parallel Studio XE 2018.1
(Tue Jan 23 2018 - 12:24:20 PST)
[AMBER] Amber16+AT17: Several checks failing w/Intel Parallel Studio XE 2018.1
(Tue Jan 23 2018 - 12:18:30 PST)
Paul Meister
[AMBER] MD run saving only 250 frames
(Tue Jan 16 2018 - 11:58:00 PST)
Pengfei Li
Re: [AMBER] Regarding error in preparation of HEME via MCPB.py
(Wed Jan 31 2018 - 07:37:11 PST)
Re: [AMBER] MCPB.py error with ion id
(Wed Jan 31 2018 - 07:36:12 PST)
Re: [AMBER] KeyError: 'HIE-HD1' MCPB.py
(Thu Jan 25 2018 - 10:39:40 PST)
Re: [AMBER] Regarding error in preparation of HEME via MCPB.py
(Thu Jan 25 2018 - 10:34:38 PST)
Re: [AMBER] MCPB
(Fri Jan 19 2018 - 11:21:05 PST)
Re: [AMBER] error 12-6-4 LJ with the last update (November 2017)
(Tue Jan 16 2018 - 14:01:32 PST)
Re: [AMBER] error 12-6-4 LJ with the last update (November 2017)
(Tue Jan 16 2018 - 13:54:47 PST)
Re: [AMBER] Regarding error in preparation of HEME via MCPB.py
(Tue Jan 16 2018 - 12:07:04 PST)
Re: [AMBER] Amber 16.12 and 12-6-4 force field Problem
(Sat Jan 13 2018 - 18:40:07 PST)
Qinghua Liao
Re: [AMBER] QM/MM metadynamics with external QM code
(Fri Jan 26 2018 - 04:05:53 PST)
Re: [AMBER] QM/MM metadynamics with external QM code
(Fri Jan 26 2018 - 02:36:47 PST)
[AMBER] QM/MM metadynamics with external QM code
(Fri Jan 26 2018 - 01:42:22 PST)
Re: [AMBER] Amber 18
(Fri Jan 19 2018 - 07:32:36 PST)
[AMBER] Amber 18
(Fri Jan 19 2018 - 04:47:44 PST)
Re: [AMBER] error 12-6-4 LJ with the last update (November 2017)
(Thu Jan 11 2018 - 05:51:52 PST)
Re: [AMBER] gnuplot x-axis represented the number of frames how to convert it in nano second time.
(Wed Jan 10 2018 - 05:47:34 PST)
Re: [AMBER] AMBER intelmpi installation on cluster
(Tue Jan 02 2018 - 02:30:24 PST)
Rana Rehan Khalid
Re: [AMBER] gnuplot x-axis represented the number of frames how to convert it in nano second time.
(Wed Jan 10 2018 - 07:02:00 PST)
Re: [AMBER] gnuplot x-axis represented the number of frames how to convert it in nano second time.
(Wed Jan 10 2018 - 06:53:21 PST)
[AMBER] gnuplot x-axis represented the number of frames how to convert it in nano second time.
(Wed Jan 10 2018 - 05:44:48 PST)
Re: [AMBER] xmgr x-axis change to ns.
(Sun Jan 07 2018 - 09:25:41 PST)
Re: [AMBER] xmgr x-axis change to ns.
(Sun Jan 07 2018 - 06:55:43 PST)
[AMBER] xmgr x-axis change to ns.
(Sat Jan 06 2018 - 08:30:31 PST)
Ray Luo
Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB 3C
(Fri Jan 19 2018 - 15:57:11 PST)
roja rahmani
Re: [AMBER] Empty .frcmod file
(Tue Jan 30 2018 - 08:15:59 PST)
Re: [AMBER] Empty .frcmod file
(Tue Jan 30 2018 - 08:09:18 PST)
Re: [AMBER] Empty .frcmod file
(Tue Jan 30 2018 - 06:50:10 PST)
Re: [AMBER] Empty .frcmod file
(Tue Jan 30 2018 - 06:20:11 PST)
Re: [AMBER] Empty .frcmod file
(Tue Jan 30 2018 - 06:19:16 PST)
[AMBER] Empty .frcmod file
(Tue Jan 30 2018 - 05:39:56 PST)
Roma Mukhopadhyay
[AMBER] Replica exchange thermodynamic integration in AMBER
(Thu Jan 11 2018 - 15:45:55 PST)
Ross Walker
Re: [AMBER] Amber 16.12 and 12-6-4 force field Problem
(Sat Jan 13 2018 - 20:19:32 PST)
Re: [AMBER] Amber 16.12 and 12-6-4 force field Problem
(Sat Jan 13 2018 - 12:10:01 PST)
Re: [AMBER] LIPID17 reference ?
(Wed Jan 03 2018 - 06:32:42 PST)
Ruth Helena Tichauer
Re: [AMBER] QM/MM SMD with 'external' theory and PBCs
(Fri Jan 26 2018 - 21:40:46 PST)
[AMBER] QM/MM SMD with 'external' theory and PBCs
(Fri Jan 26 2018 - 06:33:05 PST)
Saikat Pal
[AMBER] cpptraj.OMP vs cpptraj
(Wed Jan 10 2018 - 03:06:25 PST)
Re: [AMBER] Problem regarding compiling in cpptraj with openmp
(Thu Jan 04 2018 - 23:32:17 PST)
[AMBER] Problem regarding compiling in cpptraj with openmp
(Thu Jan 04 2018 - 22:54:54 PST)
Saman Yousuf ali
[AMBER] fatty acid ligand comes out of binding site during md.
(Sat Jan 20 2018 - 05:43:11 PST)
Sandip Mondal
[AMBER] MMGBSA calculation gives very high positive free energy of binding!!!
(Thu Jan 11 2018 - 01:41:12 PST)
Scott Brozell
Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber
(Mon Jan 29 2018 - 13:49:15 PST)
Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber
(Mon Jan 29 2018 - 11:56:28 PST)
Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber
(Fri Jan 26 2018 - 12:09:07 PST)
Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber
(Fri Jan 26 2018 - 10:40:41 PST)
Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber
(Thu Jan 25 2018 - 10:51:01 PST)
Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber
(Tue Jan 23 2018 - 16:13:24 PST)
Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber
(Tue Jan 23 2018 - 12:12:14 PST)
Setyanto Md
Re: [AMBER] Compressing trajectory file
(Tue Jan 30 2018 - 22:37:32 PST)
[AMBER] Compressing trajectory file
(Fri Jan 26 2018 - 04:16:07 PST)
SHALJA VERMA
Re: [AMBER] command not working
(Mon Jan 29 2018 - 05:50:38 PST)
[AMBER] command not working
(Mon Jan 29 2018 - 02:28:34 PST)
[AMBER] command problem
(Mon Jan 29 2018 - 02:27:46 PST)
Shamsi, Zahra
[AMBER] Is there anyway to recover the potential energies obtained after running md
(Wed Jan 31 2018 - 08:20:57 PST)
Siddhartha Jain
Re: [AMBER] GBSA parameters
(Sun Jan 28 2018 - 13:09:06 PST)
Re: [AMBER] GBSA parameters
(Sun Jan 28 2018 - 11:22:32 PST)
[AMBER] GBSA parameters
(Sat Jan 27 2018 - 17:11:57 PST)
[AMBER] Transformation from cartesian to torsion space
(Mon Jan 22 2018 - 12:00:39 PST)
Simon Kit Sang Chu
Re: [AMBER] cpptraj long writing queue
(Wed Jan 24 2018 - 06:40:32 PST)
[AMBER] cpptraj long writing queue
(Wed Jan 24 2018 - 00:03:49 PST)
[AMBER] Writing mdcrd to inpcrd
(Mon Jan 22 2018 - 03:29:09 PST)
Re: [AMBER] AMBER intelmpi installation on cluster
(Tue Jan 02 2018 - 19:48:28 PST)
[AMBER] AMBER intelmpi installation on cluster
(Mon Jan 01 2018 - 22:31:51 PST)
Stregone
[AMBER] EVB xch_* values
(Tue Jan 23 2018 - 11:44:07 PST)
Suman Bhaumik
[AMBER] PROBLEM ENCOUNTERED WHILE UNDERGOING TUTUORIAL FOR ROOM TEMPERATURE IONIC LIQUID.
(Sun Jan 21 2018 - 01:46:05 PST)
Sundar
Re: [AMBER] Avoiding pdb4amber renumbering
(Tue Jan 23 2018 - 12:55:32 PST)
[AMBER] Avoiding pdb4amber renumbering
(Tue Jan 23 2018 - 10:04:22 PST)
Szymon Żaczek
Re: [AMBER] leap
(Tue Jan 16 2018 - 11:32:33 PST)
Re: [AMBER] Fwd: Hydrophobic interaction VS time in protein interfaces
(Mon Jan 15 2018 - 03:10:45 PST)
Thakur, Abhishek
Re: [AMBER] MCPB.py error with ion id
(Wed Jan 31 2018 - 08:54:07 PST)
[AMBER] MCPB.py error with ion id
(Mon Jan 29 2018 - 07:37:07 PST)
[AMBER] KeyError: 'HIE-HD1' MCPB.py
(Wed Jan 24 2018 - 12:43:10 PST)
[AMBER] MCPB
(Thu Jan 18 2018 - 14:23:49 PST)
Re: [AMBER] QM/MM MD B3LYP
(Wed Jan 10 2018 - 10:02:51 PST)
[AMBER] QM/MM MD B3LYP
(Wed Jan 10 2018 - 09:35:29 PST)
[AMBER] QM/MM MD B3LYP
(Wed Jan 10 2018 - 09:25:05 PST)
Re: [AMBER] use_template = 0
(Wed Jan 10 2018 - 09:04:20 PST)
Re: [AMBER] use_template = 0
(Wed Jan 10 2018 - 09:02:54 PST)
[AMBER] use_template = 0
(Wed Jan 10 2018 - 08:34:27 PST)
Re: [AMBER] qm2_extern_gau_module
(Tue Jan 09 2018 - 09:11:29 PST)
Re: [AMBER] qm2_extern_gau_module
(Tue Jan 09 2018 - 08:49:59 PST)
Re: [AMBER] qm2_extern_gau_module
(Fri Jan 05 2018 - 12:12:03 PST)
[AMBER] qm2_extern_gau_module
(Fri Jan 05 2018 - 11:46:50 PST)
Thomas Exner
Re: [AMBER] Density equilibration
(Sat Jan 06 2018 - 04:23:48 PST)
[AMBER] Density equilibration
(Fri Jan 05 2018 - 07:21:47 PST)
Thomas Fox
Re: [AMBER] pmemd.cuda and rigid CH2Cl2
(Fri Jan 12 2018 - 00:38:48 PST)
Vatsal Purohit
[AMBER] Ligand modifying softwares.
(Thu Jan 18 2018 - 20:23:21 PST)
Veronika Jurásková
Re: [AMBER] Non-PBC simulation in a droplet made of organic solvent
(Wed Jan 24 2018 - 02:45:23 PST)
[AMBER] Non-PBC simulation in a droplet made of organic solvent
(Mon Jan 22 2018 - 02:13:49 PST)
Vlad Cojocaru
Re: [AMBER] Query regarding the ff99SB*ildn force field
(Wed Jan 31 2018 - 05:55:45 PST)
Yuan Hu
Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber
(Tue Jan 30 2018 - 07:09:16 PST)
Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber
(Mon Jan 29 2018 - 12:35:45 PST)
Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber
(Fri Jan 26 2018 - 12:15:53 PST)
Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber
(Fri Jan 26 2018 - 11:50:44 PST)
Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber
(Fri Jan 26 2018 - 11:43:06 PST)
Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber
(Fri Jan 26 2018 - 05:17:29 PST)
Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber
(Wed Jan 24 2018 - 05:19:13 PST)
Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber
(Tue Jan 23 2018 - 19:06:11 PST)
Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber
(Tue Jan 23 2018 - 13:27:41 PST)
Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber
(Mon Jan 22 2018 - 22:41:28 PST)
[AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber
(Mon Jan 22 2018 - 16:03:01 PST)
Yuliana Bosken
Re: [AMBER] parmchk
(Sun Jan 28 2018 - 05:01:42 PST)
[AMBER] parmchk
(Sat Jan 27 2018 - 20:18:41 PST)
Re: [AMBER] Crystal water in Amber 16
(Sun Jan 21 2018 - 13:14:33 PST)
Re: [AMBER] Crystal water in Amber 16
(Thu Jan 18 2018 - 04:33:10 PST)
[AMBER] Crystal water in Amber 16
(Wed Jan 17 2018 - 21:12:45 PST)
姚永霖
[AMBER] CPPTRAJ HBond analysis Segmentation fault (core dumped)
(Thu Jan 25 2018 - 17:33:30 PST)
[AMBER] CPPTRAJ HBond analysis Segmentation fault (core dumped)
(Thu Jan 25 2018 - 06:54:00 PST)
巩梦雪
Re: [AMBER] How to perform Newton-Raphson minimization to protein
(Fri Jan 26 2018 - 01:38:55 PST)
[AMBER] How to perform Newton-Raphson minimization to protein
(Mon Jan 22 2018 - 23:30:22 PST)
Last message date
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Wed Jan 31 2018 - 10:00:02 PST
Archived on
: Fri Nov 29 2024 - 05:55:37 PST
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