Amber Archive Jul 2019 by author
379 messages
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Starting
Mon Jul 01 2019 - 04:00:02 PDT,
Ending
Wed Jul 31 2019 - 13:30:03 PDT
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A K
Re: [AMBER] problem with building cpptraj in AmberTools19
(Mon Jul 29 2019 - 12:26:18 PDT)
Re: [AMBER] problem with building cpptraj in AmberTools19
(Mon Jul 29 2019 - 10:50:04 PDT)
Re: [AMBER] problem with building cpptraj in AmberTools19
(Thu Jul 25 2019 - 14:26:25 PDT)
Re: [AMBER] Error with make test after installing Amber14 and AmberTools15
(Thu Jul 18 2019 - 07:04:18 PDT)
[AMBER] Error with make test after installing Amber14 and AmberTools15
(Wed Jul 17 2019 - 17:30:05 PDT)
Aashish Bhatt
Re: [AMBER] Error in saving prmtop and inpcrd
(Fri Jul 12 2019 - 02:26:55 PDT)
ABEL Stephane
Re: [AMBER] How to change the coordinates of the system
(Mon Jul 15 2019 - 07:06:24 PDT)
Re: [AMBER] R . E. D
(Tue Jul 02 2019 - 11:03:29 PDT)
Re: [AMBER] R . E. D
(Tue Jul 02 2019 - 10:28:30 PDT)
Ahmed Elrashedy
Re: [AMBER] Parameter file for GTP or GMP containing tRNA
(Mon Jul 22 2019 - 03:20:06 PDT)
Akinpelu Olayinka
[AMBER] Problem running Antechamber for GTP
(Wed Jul 31 2019 - 11:12:37 PDT)
Alan
Re: [AMBER] About -dr option in Antechamber
(Wed Jul 10 2019 - 14:25:35 PDT)
[AMBER] About -dr option in Antechamber
(Wed Jul 10 2019 - 04:53:19 PDT)
Alessandro LANDI
Re: [AMBER] Recent Force Fields for nucleotides
(Wed Jul 17 2019 - 02:24:02 PDT)
[AMBER] Recent Force Fields for nucleotides
(Tue Jul 16 2019 - 04:11:14 PDT)
Aliakbartehrani Zahra
[AMBER] question about GIST calculation
(Tue Jul 30 2019 - 03:17:04 PDT)
Amen Shamim
[AMBER] Export command not found (export CUDA_VISIBLE_DEVICES)
(Mon Jul 08 2019 - 11:05:54 PDT)
Amit Kumar
[AMBER] Kinetic Energy is zero in production run.
(Sat Jul 27 2019 - 04:38:18 PDT)
Anthony Bogetti
Re: [AMBER] There is a bond of 8.882728 angstroms between: [Blank]
(Tue Jul 09 2019 - 10:34:58 PDT)
Re: [AMBER] There is a bond of 8.882728 angstroms between: [Blank]
(Tue Jul 09 2019 - 08:52:26 PDT)
Re: [AMBER] There is a bond of 8.882728 angstroms between: [Blank]
(Tue Jul 09 2019 - 08:49:23 PDT)
[AMBER] There is a bond of 8.882728 angstroms between: [Blank]
(Tue Jul 09 2019 - 08:40:58 PDT)
Anuja Ware
[AMBER] Adding Na+
(Wed Jul 17 2019 - 08:21:03 PDT)
Aswin Hanagal
[AMBER] Significant deviation in electrostatics, (EEL/EGL values)
(Wed Jul 10 2019 - 08:11:56 PDT)
ATUL KUMAR
Re: [AMBER] Fwd:
(Tue Jul 09 2019 - 06:47:49 PDT)
Bacaita Simona
[AMBER] install Amber16
(Wed Jul 03 2019 - 04:47:53 PDT)
Bharat Manna
[AMBER] Query on linear interaction energy (lie) calculation using CPPTRAJ
(Wed Jul 24 2019 - 21:49:16 PDT)
Bill Ross
Re: [AMBER] Error in preparing system using AmberTools19
(Sun Jul 28 2019 - 22:19:46 PDT)
Re: [AMBER] Error in preparing system using AmberTools19
(Tue Jul 23 2019 - 00:19:14 PDT)
Re: [AMBER] Error in preparing system using AmberTools19
(Tue Jul 23 2019 - 00:18:35 PDT)
Re: [AMBER] Error in preparing system using AmberTools19
(Tue Jul 23 2019 - 00:13:52 PDT)
Re: [AMBER] Error in preparing system using AmberTools19
(Mon Jul 22 2019 - 12:50:10 PDT)
[AMBER] Posits preparing to pounce on Floating Point
(Wed Jul 17 2019 - 20:29:52 PDT)
Re: [AMBER] CUDA errors on a 700k system
(Sun Jul 14 2019 - 11:07:55 PDT)
Re: [AMBER] Fwd:
(Tue Jul 09 2019 - 01:58:07 PDT)
Re: [AMBER] Export command not found (export CUDA_VISIBLE_DEVICES)
(Mon Jul 08 2019 - 13:40:56 PDT)
Re: [AMBER] Fwd:
(Sat Jul 06 2019 - 05:23:13 PDT)
Re: [AMBER] Fwd:
(Sat Jul 06 2019 - 05:20:30 PDT)
Re: [AMBER] Fwd: amber installation problem
(Sat Jul 06 2019 - 03:32:51 PDT)
Biplab Ghosh
[AMBER] How to print the total Potential Energy for an atom?
(Thu Jul 04 2019 - 02:09:05 PDT)
Bowman, Jacob
Re: [AMBER] EPW "ATOMS Moving too fast" - TIP4PEW
(Mon Jul 08 2019 - 10:33:24 PDT)
[AMBER] EPW "ATOMS Moving too fast" - TIP4PEW
(Mon Jul 08 2019 - 10:25:03 PDT)
Carlos Simmerling
Re: [AMBER] There is a bond of 8.882728 angstroms between: [Blank]
(Tue Jul 09 2019 - 10:04:15 PDT)
Re: [AMBER] There is a bond of 8.882728 angstroms between: [Blank]
(Tue Jul 09 2019 - 09:15:54 PDT)
Re: [AMBER] There is a bond of 8.882728 angstroms between: [Blank]
(Tue Jul 09 2019 - 08:43:42 PDT)
Re: [AMBER] amber14sb.ff
(Tue Jul 09 2019 - 08:26:39 PDT)
Re: [AMBER] EPW "ATOMS Moving too fast" - TIP4PEW
(Mon Jul 08 2019 - 11:41:15 PDT)
Re: [AMBER] EPW "ATOMS Moving too fast" - TIP4PEW
(Mon Jul 08 2019 - 10:29:40 PDT)
Charu Sharma (JRF)
[AMBER] Fwd:
(Tue Jul 09 2019 - 06:43:31 PDT)
[AMBER] Fwd: Fwd:
(Tue Jul 09 2019 - 04:08:47 PDT)
Re: [AMBER] Fwd:
(Tue Jul 09 2019 - 04:02:23 PDT)
[AMBER] Fwd:
(Tue Jul 09 2019 - 01:08:47 PDT)
[AMBER] Fwd:
(Sat Jul 06 2019 - 04:20:57 PDT)
Re: [AMBER] Fwd: amber installation problem
(Sat Jul 06 2019 - 04:08:23 PDT)
Re: [AMBER] Fwd: amber installation problem
(Sat Jul 06 2019 - 03:23:29 PDT)
Re: [AMBER] Fwd: amber installation problem
(Sat Jul 06 2019 - 03:24:15 PDT)
Re: [AMBER] Fwd: amber installation problem
(Sat Jul 06 2019 - 00:49:35 PDT)
Re: [AMBER] Fwd: amber installation problem
(Sat Jul 06 2019 - 00:34:35 PDT)
[AMBER] Fwd: amber installation problem
(Sat Jul 06 2019 - 00:26:21 PDT)
[AMBER] Fwd: Fwd: please clarify this answer
(Wed Jul 03 2019 - 10:22:52 PDT)
Chen, Wei
Re: [AMBER] missing bond parameter for Mg ion
(Tue Jul 30 2019 - 15:04:32 PDT)
[AMBER] missing bond parameter for Mg ion
(Mon Jul 29 2019 - 14:35:22 PDT)
Chetna Tyagi
Re: [AMBER] Reference for External electric field implementation in Amber
(Wed Jul 24 2019 - 04:44:49 PDT)
Re: [AMBER] Combing trajectoty
(Wed Jul 24 2019 - 04:29:59 PDT)
Re: [AMBER] Can't load trajectory in coordinate formate from amber in VMD
(Wed Jul 24 2019 - 04:21:56 PDT)
Re: [AMBER] Reference for External electric field implementation in Amber
(Wed Jul 24 2019 - 04:17:46 PDT)
cpimenta
[AMBER] GROMACS to AMBER .top and .pdb conversion using gromber
(Sat Jul 06 2019 - 04:56:44 PDT)
CROUZY Serge 119222
[AMBER] Large increase in polarization energy during MD
(Tue Jul 23 2019 - 04:39:59 PDT)
Cruzeiro, Vinicius
Re: [AMBER] Error: "Bad data for namelist object statene" with constant pH RE simulation
(Sat Jul 20 2019 - 11:03:14 PDT)
Daniel Roe
Re: [AMBER] problem with building cpptraj in AmberTools19
(Wed Jul 31 2019 - 05:09:58 PDT)
Re: [AMBER] problem with building cpptraj in AmberTools19
(Mon Jul 29 2019 - 12:10:07 PDT)
Re: [AMBER] Regarding cut-off distance in hydrogen bond
(Mon Jul 29 2019 - 06:11:41 PDT)
Re: [AMBER] problem with building cpptraj in AmberTools19
(Wed Jul 24 2019 - 12:01:19 PDT)
Re: [AMBER] Calculating area per lipid for system with different numbers of lipids on leaflets
(Tue Jul 23 2019 - 09:15:52 PDT)
Re: [AMBER] How to change the coordinates of the system
(Fri Jul 19 2019 - 05:10:22 PDT)
Re: [AMBER] How to change the coordinates of the system
(Fri Jul 19 2019 - 02:13:59 PDT)
Re: [AMBER] Print out velocities from a restart-crd file
(Thu Jul 18 2019 - 05:07:31 PDT)
Re: [AMBER] How to change the coordinates of the system
(Mon Jul 15 2019 - 07:39:06 PDT)
Re: [AMBER] Trajout by distance
(Mon Jul 15 2019 - 06:31:32 PDT)
Re: [AMBER] How to change the coordinates of the system
(Mon Jul 15 2019 - 06:26:36 PDT)
Re: [AMBER] closest distance between ligand and particular amino-acid residues during MD simulation
(Mon Jul 08 2019 - 06:32:10 PDT)
Re: [AMBER] Error in prmtop and inpcrd atom
(Mon Jul 08 2019 - 06:28:17 PDT)
David A Case
Re: [AMBER] Problem running Antechamber for GTP
(Wed Jul 31 2019 - 13:17:46 PDT)
Re: [AMBER] Non-standard Hydrogen Bonding
(Tue Jul 30 2019 - 13:11:34 PDT)
Re: [AMBER] missing bond parameter for Mg ion
(Tue Jul 30 2019 - 07:53:01 PDT)
Re: [AMBER] MMPBSA for Absolute free energy
(Fri Jul 26 2019 - 12:21:47 PDT)
Re: [AMBER] Amber installation problem
(Fri Jul 26 2019 - 05:42:40 PDT)
Re: [AMBER] reg: residue number order like pdb
(Fri Jul 26 2019 - 05:33:01 PDT)
Re: [AMBER] How to prepare correct gaussian input for RESP charge calculation?
(Thu Jul 18 2019 - 05:22:51 PDT)
Re: [AMBER] Error with make test after installing Amber14 and AmberTools15
(Thu Jul 18 2019 - 05:16:19 PDT)
Re: [AMBER] Adding Na+
(Wed Jul 17 2019 - 09:34:24 PDT)
Re: [AMBER] Covariance Matrix of residues center of mass
(Wed Jul 17 2019 - 09:30:56 PDT)
Re: [AMBER] Problem with barostat during the production stage (membrane simulation)
(Wed Jul 17 2019 - 09:18:03 PDT)
Re: [AMBER] Recent Force Fields for nucleotides
(Tue Jul 16 2019 - 12:26:13 PDT)
Re: [AMBER] close contact between atoms
(Tue Jul 16 2019 - 04:34:16 PDT)
Re: [AMBER] Force field for Cecl3, Lacl3 and Prcl3
(Mon Jul 15 2019 - 04:30:45 PDT)
Re: [AMBER] Error in saving prmtop and inpcrd
(Mon Jul 15 2019 - 04:21:37 PDT)
Re: [AMBER] Glycan naming problem
(Fri Jul 05 2019 - 08:01:23 PDT)
Re: [AMBER] How to print the total Potential Energy for an atom?
(Fri Jul 05 2019 - 07:57:03 PDT)
Re: [AMBER] on the choosing of the cut-off value for PME with Amber14SB
(Wed Jul 03 2019 - 07:03:11 PDT)
Re: [AMBER] Modeling of flexible enzyme: on the selection of the thermostat
(Wed Jul 03 2019 - 06:54:15 PDT)
Re: [AMBER] SIGSEVV error on test_at_serial for QMMM interface and miniconda installation problem thrugh amberTools
(Wed Jul 03 2019 - 05:04:36 PDT)
Re: [AMBER] RESTARTED DUE TO LINMIN FAILURE
(Wed Jul 03 2019 - 04:49:25 PDT)
Re: [AMBER] R . E. D
(Tue Jul 02 2019 - 10:05:00 PDT)
Re: [AMBER] REMD error
(Tue Jul 02 2019 - 06:01:15 PDT)
Re: [AMBER] Antechamber Charge Methods
(Mon Jul 01 2019 - 13:20:06 PDT)
Re: [AMBER] Regarding nmode error
(Mon Jul 01 2019 - 05:57:14 PDT)
David Case
Re: [AMBER] Switch function in NAMDEnergy cooresponds to AMBER input flag
(Sat Jul 27 2019 - 06:08:52 PDT)
Re: [AMBER] -regarding failure in addition of Na+ ions in tleap
(Wed Jul 24 2019 - 10:24:44 PDT)
[AMBER] problem with building cpptraj in AmberTools19
(Wed Jul 24 2019 - 10:17:52 PDT)
Re: [AMBER] Large increase in polarization energy during MD
(Tue Jul 23 2019 - 15:16:49 PDT)
Re: [AMBER] Error in preparing system using AmberTools19
(Tue Jul 23 2019 - 15:10:14 PDT)
Re: [AMBER] Error in preparing system using AmberTools19
(Mon Jul 22 2019 - 13:39:21 PDT)
Re: [AMBER] Ligand-Resp-Gaussian
(Mon Jul 22 2019 - 13:33:51 PDT)
Re: [AMBER] Problem with Phenylphosphonic acid
(Sun Jul 14 2019 - 05:50:51 PDT)
Re: [AMBER] Error in saving prmtop and inpcrd
(Fri Jul 12 2019 - 12:36:21 PDT)
Re: [AMBER] Error in saving prmtop and inpcrd
(Fri Jul 12 2019 - 06:40:33 PDT)
Re: [AMBER] PM6 charges for MD with AMBER
(Thu Jul 11 2019 - 06:39:37 PDT)
Re: [AMBER] Compiling MPI 3D-RISM
(Wed Jul 10 2019 - 14:45:01 PDT)
Re: [AMBER] About -dr option in Antechamber
(Wed Jul 10 2019 - 09:34:38 PDT)
Re: [AMBER] There is a bond of 8.882728 angstroms between: [Blank]
(Wed Jul 10 2019 - 09:30:20 PDT)
Re: [AMBER] RESP charges
(Tue Jul 09 2019 - 06:28:40 PDT)
Re: [AMBER] Adding external forces to amber
(Tue Jul 09 2019 - 06:27:10 PDT)
Re: [AMBER] EPW "ATOMS Moving too fast" - TIP4PEW
(Mon Jul 08 2019 - 15:02:49 PDT)
Re: [AMBER] parmchk2 and acceptable penalty score
(Mon Jul 08 2019 - 08:27:13 PDT)
Re: [AMBER] Perturbing residue co-ordinates within a solvated truncated octohedral box
(Sun Jul 07 2019 - 04:34:41 PDT)
Re: [AMBER] SIGSEVV error on test_at_serial for QMMM
(Fri Jul 05 2019 - 05:33:04 PDT)
Re: [AMBER] install Amber16
(Fri Jul 05 2019 - 05:16:47 PDT)
[AMBER] Problems with the miniconda installation
(Wed Jul 03 2019 - 11:34:05 PDT)
Re: [AMBER] Fwd: Fwd: please clarify this answer
(Wed Jul 03 2019 - 10:48:02 PDT)
Re: [AMBER] Error in prmtop and inpcrd atom
(Wed Jul 03 2019 - 10:44:59 PDT)
David Cerutti
Re: [AMBER] Problems with RTX2080Ti
(Tue Jul 23 2019 - 15:26:36 PDT)
Re: [AMBER] Confined box for implicit solvent simulations
(Tue Jul 23 2019 - 12:42:48 PDT)
Re: [AMBER] Problems with RTX2080Ti
(Tue Jul 23 2019 - 11:53:08 PDT)
Re: [AMBER] Confined box for implicit solvent simulations
(Tue Jul 23 2019 - 11:49:37 PDT)
Re: [AMBER] Problems with RTX2080Ti
(Tue Jul 23 2019 - 09:36:56 PDT)
Re: [AMBER] Posits preparing to pounce on Floating Point
(Fri Jul 19 2019 - 10:44:02 PDT)
Re: [AMBER] Recent Force Fields for nucleotides
(Tue Jul 16 2019 - 12:29:46 PDT)
Re: [AMBER] CUDA errors on a 700k system
(Sun Jul 14 2019 - 14:25:53 PDT)
Re: [AMBER] There is a bond of 8.882728 angstroms between: [Blank]
(Tue Jul 09 2019 - 09:34:23 PDT)
Re: [AMBER] There is a bond of 8.882728 angstroms between: [Blank]
(Tue Jul 09 2019 - 08:44:19 PDT)
Re: [AMBER] amber14sb.ff
(Tue Jul 09 2019 - 07:53:48 PDT)
Re: [AMBER] RESP charge calculation
(Mon Jul 01 2019 - 12:38:15 PDT)
Re: [AMBER] RESP charge calculation
(Mon Jul 01 2019 - 09:56:40 PDT)
Debasish Mandal
[AMBER] Amber installation problem
(Fri Jul 26 2019 - 03:03:25 PDT)
Divya Rai
[AMBER] MCPB.py showing error in the step: MCPB.py -i 1OKL.in -s 2
(Wed Jul 31 2019 - 05:09:24 PDT)
Dmitry Suplatov
[AMBER] CUDA errors on a 700k system
(Sun Jul 14 2019 - 11:00:51 PDT)
Dow Hurst
Re: [AMBER] memtestG80 alternative ? - testing actual GPUs regarding soft errors
(Mon Jul 15 2019 - 11:32:21 PDT)
Dr. Anselm Horn
[AMBER] Hydrogen atomic charges of PRO
(Thu Jul 18 2019 - 07:00:55 PDT)
Re: [AMBER] How to prepare correct gaussian input for RESP charge calculation?
(Thu Jul 18 2019 - 06:24:54 PDT)
Re: [AMBER] Glycan naming problem
(Thu Jul 04 2019 - 04:42:37 PDT)
Dylan Tasse
Re: [AMBER] amber14sb.ff
(Tue Jul 09 2019 - 08:00:39 PDT)
[AMBER] amber14sb.ff
(Tue Jul 09 2019 - 07:41:45 PDT)
[AMBER] Amberff14sb
(Tue Jul 02 2019 - 07:52:07 PDT)
Elvis Martis
Re: [AMBER] RESP charge calculation
(Mon Jul 01 2019 - 04:21:09 PDT)
Elvis Martis
Re: [AMBER] Error in preparing system using AmberTools19
(Tue Jul 23 2019 - 00:17:53 PDT)
Re: [AMBER] close contact between atoms
(Tue Jul 16 2019 - 19:30:36 PDT)
Re: [AMBER] Error in saving prmtop and inpcrd
(Fri Jul 12 2019 - 21:54:36 PDT)
Re: [AMBER] Error in saving prmtop and inpcrd
(Fri Jul 12 2019 - 21:22:43 PDT)
Re: [AMBER] Error in saving prmtop and inpcrd
(Fri Jul 12 2019 - 02:34:22 PDT)
Re: [AMBER] Error in saving prmtop and inpcrd
(Fri Jul 12 2019 - 02:14:44 PDT)
Re: [AMBER] Cluster Analysis with CPPTRAJ
(Wed Jul 10 2019 - 22:14:57 PDT)
Re: [AMBER] Cluster Analysis with CPPTRAJ
(Wed Jul 10 2019 - 20:09:07 PDT)
Re: [AMBER] Fwd:
(Tue Jul 09 2019 - 05:06:08 PDT)
Re: [AMBER] Error in prmtop and inpcrd atom
(Mon Jul 08 2019 - 21:43:39 PDT)
Re: [AMBER] Fwd:
(Sat Jul 06 2019 - 04:34:47 PDT)
Re: [AMBER] Fwd: amber installation problem
(Sat Jul 06 2019 - 04:15:51 PDT)
Re: [AMBER] Fwd: amber installation problem
(Sat Jul 06 2019 - 00:54:25 PDT)
Re: [AMBER] Fwd: amber installation problem
(Sat Jul 06 2019 - 00:44:28 PDT)
[AMBER] Fwd: amber installation problem
(Sat Jul 06 2019 - 00:32:51 PDT)
Re: [AMBER] RESP charge calculation
(Mon Jul 01 2019 - 08:24:42 PDT)
emanuele falbo
Re: [AMBER] Adding Na+
(Wed Jul 17 2019 - 09:40:22 PDT)
[AMBER] Umbrella Sampling: frequency restraint
(Wed Jul 17 2019 - 02:21:35 PDT)
Eugene huh
[AMBER] Thermodynamic information of RISM
(Mon Jul 01 2019 - 04:12:20 PDT)
Federico Olivieri
[AMBER] Swarms-of-trajectories example files
(Sun Jul 28 2019 - 18:34:12 PDT)
Felipe Franco
[AMBER] Print out velocities from a restart-crd file
(Wed Jul 17 2019 - 04:36:15 PDT)
Feng Pan
Re: [AMBER] Swarms-of-trajectories example files
(Tue Jul 30 2019 - 08:13:44 PDT)
Francesca Lønstad Bleken
Re: [AMBER] SIGSEVV error on test_at_serial for QMMM
(Wed Jul 03 2019 - 22:42:38 PDT)
[AMBER] SIGSEVV error on test_at_serial for QMMM interface and miniconda installation problem thrugh amberTools
(Wed Jul 03 2019 - 01:28:11 PDT)
Fransiska Kurniawan
[AMBER] error in mmpbsa
(Fri Jul 19 2019 - 02:24:16 PDT)
Giovanni Grazioso
Re: [AMBER] Problems with RTX2080Ti
(Tue Jul 23 2019 - 09:56:59 PDT)
[AMBER] Problems with RTX2080Ti
(Tue Jul 23 2019 - 05:55:58 PDT)
Gould, Ian R
Re: [AMBER] MD Simulation in DMSO
(Tue Jul 02 2019 - 01:23:24 PDT)
Guadalupe Alvarez
Re: [AMBER] Covariance Matrix of residues center of mass
(Thu Jul 18 2019 - 09:51:39 PDT)
[AMBER] Covariance Matrix of residues center of mass
(Wed Jul 17 2019 - 07:42:01 PDT)
Gustaf Olsson
Re: [AMBER] Problem with Phenylphosphonic acid
(Tue Jul 30 2019 - 03:43:46 PDT)
Re: [AMBER] Problem with Phenylphosphonic acid
(Sat Jul 20 2019 - 04:51:12 PDT)
[AMBER] Problem with Phenylphosphonic acid
(Fri Jul 12 2019 - 06:15:34 PDT)
Re: [AMBER] Fwd:
(Mon Jul 08 2019 - 02:10:31 PDT)
Re: [AMBER] How to replicate the number of lipids in bilayer for membrane dynamics
(Fri Jul 05 2019 - 04:10:17 PDT)
Re: [AMBER] Error: "System must be very inhomogeneous"
(Mon Jul 01 2019 - 22:16:38 PDT)
Re: [AMBER] AMBER G09 RESP Calculation problem
(Mon Jul 01 2019 - 05:07:30 PDT)
[AMBER] AMBER G09 RESP Calculation problem
(Mon Jul 01 2019 - 04:22:54 PDT)
Hai Nguyen
Re: [AMBER] unwrap in pytraj?
(Tue Jul 02 2019 - 15:13:46 PDT)
Re: [AMBER] unwrap in pytraj?
(Tue Jul 02 2019 - 13:57:52 PDT)
Hosein Geraili Daronkola
Re: [AMBER] TI for mutation of charged residues
(Tue Jul 30 2019 - 01:33:24 PDT)
[AMBER] TI for mutation of charged residues
(Mon Jul 29 2019 - 00:17:05 PDT)
James Kress
Re: [AMBER] Error in preparing system using AmberTools19
(Mon Jul 22 2019 - 10:55:16 PDT)
James Starlight
Re: [AMBER] Modeling of flexible enzyme: on the selection of the thermostat
(Thu Jul 04 2019 - 01:05:38 PDT)
Re: [AMBER] Modeling of flexible enzyme: on the selection of the thermostat
(Wed Jul 03 2019 - 06:59:01 PDT)
[AMBER] on the choosing of the cut-off value for PME with Amber14SB
(Wed Jul 03 2019 - 06:16:52 PDT)
Re: [AMBER] Modeling of flexible enzyme: on the selection of the thermostat
(Wed Jul 03 2019 - 06:10:47 PDT)
Jardin, Christophe Dr.
[AMBER] Error: "Bad data for namelist object statene" with constant pH RE simulation
(Fri Jul 19 2019 - 04:30:12 PDT)
[AMBER] mpirun <defunct> with pmemd.cuda.MPI on EXXACT systems
(Tue Jul 09 2019 - 06:57:48 PDT)
Jingxiao Bao
[AMBER] Energy different between igb=0 and igb=6 during vacuum minimization with sander
(Fri Jul 19 2019 - 06:52:44 PDT)
Josh Berryman
Re: [AMBER] electrostatic energy of mmgbsa decomposition
(Thu Jul 11 2019 - 04:49:10 PDT)
Re: [AMBER] electrostatic energy of mmgbsa decomposition
(Wed Jul 10 2019 - 02:38:04 PDT)
Kellon Belfon
Re: [AMBER] RESP charges
(Thu Jul 11 2019 - 09:51:48 PDT)
Re: [AMBER] RESP charges
(Thu Jul 11 2019 - 07:27:23 PDT)
Re: [AMBER] RESP charges
(Thu Jul 11 2019 - 07:18:53 PDT)
Kolattukudy P. Santo
Re: [AMBER] R . E. D
(Tue Jul 02 2019 - 10:41:40 PDT)
Re: [AMBER] R . E. D
(Tue Jul 02 2019 - 10:22:27 PDT)
[AMBER] R . E. D
(Tue Jul 02 2019 - 06:47:00 PDT)
koushik kasavajhala
Re: [AMBER] REMD error
(Wed Jul 03 2019 - 14:49:51 PDT)
Re: [AMBER] REMD error
(Wed Jul 03 2019 - 14:21:52 PDT)
Re: [AMBER] REMD error
(Wed Jul 03 2019 - 13:53:44 PDT)
Re: [AMBER] REMD error
(Wed Jul 03 2019 - 12:55:59 PDT)
Re: [AMBER] REMD error
(Tue Jul 02 2019 - 13:23:29 PDT)
Re: [AMBER] REMD error
(Tue Jul 02 2019 - 08:56:32 PDT)
Kshatresh Dutta Dubey
Re: [AMBER] Reference for External electric field implementation in Amber
(Wed Jul 24 2019 - 04:55:38 PDT)
[AMBER] Reference for External electric field implementation in Amber
(Tue Jul 23 2019 - 21:15:00 PDT)
Lara rajam
[AMBER] reg: residue number order like pdb
(Thu Jul 25 2019 - 11:23:07 PDT)
Leena Aggarwal
Re: [AMBER] Query regarding 3D-RISM thermodynamic output format
(Wed Jul 10 2019 - 23:56:46 PDT)
[AMBER] Query regarding 3D-RISM thermodynamic output format
(Wed Jul 10 2019 - 23:46:08 PDT)
Lod King
[AMBER] pbsa calculation
(Mon Jul 29 2019 - 17:38:24 PDT)
[AMBER] General questions regarding MMPBSA in AMBER
(Sat Jul 27 2019 - 10:19:25 PDT)
Re: [AMBER] Switch function in NAMDEnergy cooresponds to AMBER input flag
(Sat Jul 27 2019 - 08:23:15 PDT)
Re: [AMBER] MMPBSA for Absolute free energy
(Fri Jul 26 2019 - 17:25:13 PDT)
[AMBER] Switch function in NAMDEnergy cooresponds to AMBER input flag
(Fri Jul 26 2019 - 13:38:50 PDT)
[AMBER] MMPBSA for Absolute free energy
(Fri Jul 26 2019 - 12:00:50 PDT)
Re: [AMBER] Cluster Analysis with CPPTRAJ
(Wed Jul 10 2019 - 22:02:52 PDT)
[AMBER] Cluster Analysis with CPPTRAJ
(Wed Jul 10 2019 - 19:39:45 PDT)
Loris Moretti
[AMBER] Non-standard Hydrogen Bonding
(Tue Jul 30 2019 - 05:25:46 PDT)
Luboš Plamitzer
[AMBER] Using pmemd.gem (Amoeba) with nmropt=1
(Sat Jul 27 2019 - 12:33:16 PDT)
Lucas Bandeira
[AMBER] Simulating Water-Metal Interface with NPT Ensemble
(Tue Jul 30 2019 - 12:31:32 PDT)
Re: [AMBER] Error: "System must be very inhomogeneous"
(Mon Jul 01 2019 - 09:33:42 PDT)
Marcela Madrid
Re: [AMBER] REMD error
(Wed Jul 03 2019 - 14:52:19 PDT)
Re: [AMBER] REMD error
(Wed Jul 03 2019 - 14:38:25 PDT)
Re: [AMBER] REMD error
(Wed Jul 03 2019 - 13:24:45 PDT)
Re: [AMBER] REMD error
(Wed Jul 03 2019 - 12:44:47 PDT)
Re: [AMBER] REMD error
(Tue Jul 02 2019 - 11:59:04 PDT)
Re: [AMBER] REMD error
(Tue Jul 02 2019 - 06:57:43 PDT)
[AMBER] REMD error
(Mon Jul 01 2019 - 17:13:24 PDT)
Marcos Serrou do Amaral
Re: [AMBER] Constant pH MD + HMR
(Tue Jul 30 2019 - 10:04:40 PDT)
Marek Maly
Re: [AMBER] memtestG80 alternative ? - testing actual GPUs regarding soft errors
(Wed Jul 03 2019 - 01:41:13 PDT)
[AMBER] memtestG80 alternative ? - testing actual GPUs regarding soft errors
(Tue Jul 02 2019 - 08:37:55 PDT)
Maria Bzówka
[AMBER] Calculating area per lipid for system with different numbers of lipids on leaflets
(Tue Jul 23 2019 - 02:24:03 PDT)
Re: [AMBER] How to change the coordinates of the system
(Mon Jul 22 2019 - 00:08:36 PDT)
Re: [AMBER] How to change the coordinates of the system
(Fri Jul 19 2019 - 04:34:55 PDT)
Re: [AMBER] How to change the coordinates of the system
(Fri Jul 19 2019 - 01:17:05 PDT)
Re: [AMBER] Problem with barostat during the production stage (membrane simulation)
(Wed Jul 17 2019 - 09:42:46 PDT)
[AMBER] Problem with barostat during the production stage (membrane simulation)
(Wed Jul 17 2019 - 06:10:52 PDT)
Re: [AMBER] How to change the coordinates of the system
(Mon Jul 15 2019 - 06:52:56 PDT)
[AMBER] How to change the coordinates of the system
(Mon Jul 15 2019 - 04:32:32 PDT)
[AMBER] How to replicate the number of lipids in bilayer for membrane dynamics
(Fri Jul 05 2019 - 01:46:01 PDT)
Matias Machado
Re: [AMBER] TI for mutation of charged residues
(Tue Jul 30 2019 - 12:16:05 PDT)
Re: [AMBER] Error in preparing system using AmberTools19
(Sun Jul 28 2019 - 22:51:48 PDT)
Re: [AMBER] Error in preparing system using AmberTools19
(Sun Jul 28 2019 - 22:41:19 PDT)
Re: [AMBER] Kinetic Energy is zero in production run.
(Sat Jul 27 2019 - 14:13:18 PDT)
Re: [AMBER] Error in preparing system using AmberTools19
(Wed Jul 24 2019 - 12:30:44 PDT)
Re: [AMBER] Error in preparing system using AmberTools19
(Wed Jul 24 2019 - 12:21:35 PDT)
Re: [AMBER] Error in preparing system using AmberTools19
(Wed Jul 24 2019 - 11:58:53 PDT)
Re: [AMBER] Error in preparing system using AmberTools19
(Tue Jul 23 2019 - 06:20:38 PDT)
Re: [AMBER] Error in preparing system using AmberTools19
(Mon Jul 22 2019 - 13:46:12 PDT)
Re: [AMBER] New ACPYPE server
(Fri Jul 19 2019 - 11:30:51 PDT)
Re: [AMBER] Posits preparing to pounce on Floating Point
(Fri Jul 19 2019 - 09:59:38 PDT)
Re: [AMBER] Adding Na+
(Wed Jul 17 2019 - 10:30:28 PDT)
Re: [AMBER] Recent Force Fields for nucleotides
(Tue Jul 16 2019 - 08:52:54 PDT)
Re: [AMBER] Adding external forces to amber
(Mon Jul 08 2019 - 13:13:59 PDT)
Re: [AMBER] Adding external forces to amber
(Sat Jul 06 2019 - 12:22:22 PDT)
Re: [AMBER] How to print the total Potential Energy for an atom?
(Fri Jul 05 2019 - 13:57:27 PDT)
Melania T
Re: [AMBER] Antechamber Charge Methods
(Mon Jul 01 2019 - 16:56:53 PDT)
Mohammad Hassan Khatami
Re: [AMBER] Confined box for implicit solvent simulations
(Tue Jul 23 2019 - 12:23:27 PDT)
[AMBER] Confined box for implicit solvent simulations
(Tue Jul 23 2019 - 11:10:06 PDT)
Re: [AMBER] Adding external forces to amber
(Tue Jul 09 2019 - 06:30:43 PDT)
Re: [AMBER] Adding external forces to amber
(Mon Jul 08 2019 - 06:25:22 PDT)
Re: [AMBER] Adding external forces to amber
(Sat Jul 06 2019 - 12:47:17 PDT)
[AMBER] Adding external forces to amber
(Sat Jul 06 2019 - 06:59:49 PDT)
mwli.mail.ustc.edu.cn
[AMBER] Combing trajectoty
(Tue Jul 23 2019 - 18:46:18 PDT)
Nikolay N. Kuzmich
[AMBER] Constant pH MD + HMR
(Tue Jul 09 2019 - 04:43:25 PDT)
Patil Pranita Uttamrao
[AMBER] -regarding failure in addition of Na+ ions in tleap
(Wed Jul 24 2019 - 07:26:22 PDT)
Pengfei Li
Re: [AMBER] MCPB.py generated parameters in leap
(Mon Jul 22 2019 - 18:56:01 PDT)
Re: [AMBER] MCPB.py generated parameters in leap
(Mon Jul 22 2019 - 18:55:03 PDT)
Re: [AMBER] MCPB.py generated parameters in leap
(Mon Jul 22 2019 - 18:48:21 PDT)
Re: [AMBER] MCPB.py generated parameters in leap
(Tue Jul 09 2019 - 19:45:33 PDT)
Pietro Aronica
[AMBER] Trajout by distance
(Mon Jul 15 2019 - 04:03:58 PDT)
Prajwal Nandekar
Re: [AMBER] Calculating area per lipid for system with different numbers of lipids on leaflets
(Tue Jul 23 2019 - 02:32:00 PDT)
Prasanth G, Research Scholar
[AMBER] Ligand-Resp-Gaussian
(Mon Jul 22 2019 - 09:26:31 PDT)
[AMBER] pca - Projecting vectors onto a trajectory
(Thu Jul 18 2019 - 03:40:34 PDT)
[AMBER] salt concentration in the production run and MMPBSA
(Wed Jul 10 2019 - 09:50:55 PDT)
Re: [AMBER] parmchk2 and acceptable penalty score
(Wed Jul 10 2019 - 09:37:18 PDT)
[AMBER] parmchk2 and acceptable penalty score
(Fri Jul 05 2019 - 10:08:49 PDT)
Premila Samuel Mohan Dass
Re: [AMBER] RESP charge calculation
(Mon Jul 01 2019 - 17:43:40 PDT)
Rajarshi Roy
Re: [AMBER] Regarding nmode error
(Mon Jul 01 2019 - 06:49:01 PDT)
Rakesh Srivastava
Re: [AMBER] Query regarding 3D-RISM thermodynamic output format
(Wed Jul 10 2019 - 23:51:49 PDT)
Re: [AMBER] Compiling MPI 3D-RISM
(Wed Jul 10 2019 - 11:07:51 PDT)
[AMBER] Compiling MPI 3D-RISM
(Wed Jul 10 2019 - 03:50:07 PDT)
Ray Luo
Re: [AMBER] pbsa calculation
(Mon Jul 29 2019 - 20:49:21 PDT)
richa anand
[AMBER] Regarding cut-off distance in hydrogen bond
(Sun Jul 28 2019 - 07:32:03 PDT)
Rinsha Chk
Re: [AMBER] closest distance between ligand and particular amino-acid residues during MD simulation
(Tue Jul 09 2019 - 03:20:17 PDT)
[AMBER] closest distance between ligand and particular amino-acid residues during MD simulation
(Mon Jul 08 2019 - 04:28:44 PDT)
Rodriguez, Yoel
Re: [AMBER] MD Simulation in DMSO
(Tue Jul 02 2019 - 11:43:17 PDT)
Re: [AMBER] MD Simulation in DMSO
(Tue Jul 02 2019 - 01:14:18 PDT)
Roitberg,Adrian E
Re: [AMBER] Fwd:
(Tue Jul 09 2019 - 04:06:54 PDT)
Ross Walker
Re: [AMBER] Export command not found (export CUDA_VISIBLE_DEVICES)
(Mon Jul 08 2019 - 19:24:39 PDT)
Re: [AMBER] memtestG80 alternative ? - testing actual GPUs regarding soft errors
(Tue Jul 02 2019 - 18:52:02 PDT)
Rui Chen
Re: [AMBER] Glycan naming problem
(Fri Jul 05 2019 - 08:24:56 PDT)
Re: [AMBER] Glycan naming problem
(Thu Jul 04 2019 - 09:56:37 PDT)
[AMBER] Glycan naming problem
(Wed Jul 03 2019 - 21:28:32 PDT)
Ruth Helena Tichauer
Re: [AMBER] vlimit exceeded and volume of ucell too big, too many subcells during adQM/MM dynamics
(Thu Jul 11 2019 - 00:39:25 PDT)
[AMBER] vlimit exceeded and volume of ucell too big, too many subcells during adQM/MM dynamics
(Thu Jul 11 2019 - 00:36:30 PDT)
Re: [AMBER] set RA, RT and n_partition in adQM/MM run
(Wed Jul 10 2019 - 03:41:39 PDT)
Ruxi Qi
Re: [AMBER] Issue installing Amber18 pbsa.cuda
(Wed Jul 10 2019 - 20:34:08 PDT)
Sadaf Rani
[AMBER] Error in resp charge calculation
(Mon Jul 22 2019 - 13:20:46 PDT)
Re: [AMBER] How to prepare correct gaussian input for RESP charge calculation?
(Thu Jul 18 2019 - 13:49:35 PDT)
[AMBER] How to prepare correct gaussian input for RESP charge calculation?
(Wed Jul 17 2019 - 12:03:34 PDT)
Re: [AMBER] close contact between atoms
(Tue Jul 16 2019 - 11:38:19 PDT)
[AMBER] close contact between atoms
(Mon Jul 15 2019 - 13:22:05 PDT)
Re: [AMBER] RESP charges
(Thu Jul 11 2019 - 08:49:25 PDT)
Re: [AMBER] RESP charges
(Thu Jul 11 2019 - 05:36:52 PDT)
[AMBER] RESP charges
(Sun Jul 07 2019 - 11:45:38 PDT)
Re: [AMBER] RESTARTED DUE TO LINMIN FAILURE
(Thu Jul 04 2019 - 11:59:20 PDT)
Re: [AMBER] RESTARTED DUE TO LINMIN FAILURE
(Tue Jul 02 2019 - 11:23:31 PDT)
Re: [AMBER] RESP charge calculation
(Mon Jul 01 2019 - 12:34:40 PDT)
Re: [AMBER] RESP charge calculation
(Mon Jul 01 2019 - 09:37:22 PDT)
Re: [AMBER] RESP charge calculation
(Mon Jul 01 2019 - 07:35:11 PDT)
[AMBER] RESP charge calculation
(Mon Jul 01 2019 - 03:39:39 PDT)
Santanu Santra
Re: [AMBER] Error in prmtop and inpcrd atom
(Tue Jul 09 2019 - 06:06:25 PDT)
Re: [AMBER] Error in prmtop and inpcrd atom
(Tue Jul 09 2019 - 05:34:14 PDT)
SARAH JEANNE LEFAVE
Re: [AMBER] MCPB.py generated parameters in leap
(Mon Jul 15 2019 - 15:59:42 PDT)
[AMBER] MCPB.py generated parameters in leap
(Fri Jul 05 2019 - 10:13:18 PDT)
SATYAJIT KHATUA
[AMBER] modelling of a penta coordination around zinc ion (+2) using MCPB.py
(Mon Jul 29 2019 - 22:22:50 PDT)
Satyaseelan C
Re: [AMBER] Force field for Cecl3, Lacl3 and Prcl3
(Tue Jul 16 2019 - 03:14:03 PDT)
[AMBER] Force field for Cecl3, Lacl3 and Prcl3
(Mon Jul 15 2019 - 02:04:16 PDT)
Shayna Hilburg
Re: [AMBER] unwrap in pytraj?
(Tue Jul 02 2019 - 14:32:04 PDT)
[AMBER] unwrap in pytraj?
(Tue Jul 02 2019 - 13:49:59 PDT)
Shilpa Gupta
[AMBER] Error in MMPBSA calculation
(Tue Jul 16 2019 - 00:03:02 PDT)
shivangi agarwal
Re: [AMBER] Error in preparing system using AmberTools19
(Wed Jul 31 2019 - 00:23:52 PDT)
Re: [AMBER] Error in preparing system using AmberTools19
(Sun Jul 28 2019 - 22:34:03 PDT)
Re: [AMBER] Error in preparing system using AmberTools19
(Sun Jul 28 2019 - 21:51:30 PDT)
Re: [AMBER] Error in preparing system using AmberTools19
(Tue Jul 23 2019 - 20:50:12 PDT)
Re: [AMBER] Error in preparing system using AmberTools19
(Tue Jul 23 2019 - 09:55:09 PDT)
Re: [AMBER] Error in preparing system using AmberTools19
(Tue Jul 23 2019 - 00:02:34 PDT)
Re: [AMBER] Error in preparing system using AmberTools19
(Mon Jul 22 2019 - 11:00:51 PDT)
[AMBER] Error in preparing system using AmberTools19
(Mon Jul 22 2019 - 09:29:44 PDT)
Re: [AMBER] Error in saving prmtop and inpcrd
(Sun Jul 14 2019 - 22:53:27 PDT)
Re: [AMBER] Error in saving prmtop and inpcrd
(Fri Jul 12 2019 - 21:17:39 PDT)
Re: [AMBER] Error in saving prmtop and inpcrd
(Fri Jul 12 2019 - 21:05:59 PDT)
Re: [AMBER] Error in saving prmtop and inpcrd
(Fri Jul 12 2019 - 04:15:03 PDT)
Re: [AMBER] Error in saving prmtop and inpcrd
(Fri Jul 12 2019 - 02:11:25 PDT)
[AMBER] Error in saving prmtop and inpcrd
(Fri Jul 12 2019 - 01:42:24 PDT)
Re: [AMBER] Error in prmtop and inpcrd atom
(Wed Jul 10 2019 - 00:00:37 PDT)
Re: [AMBER] Error in prmtop and inpcrd atom
(Tue Jul 09 2019 - 06:04:07 PDT)
Re: [AMBER] Error in prmtop and inpcrd atom
(Tue Jul 09 2019 - 05:45:52 PDT)
Re: [AMBER] Error in prmtop and inpcrd atom
(Mon Jul 08 2019 - 21:03:46 PDT)
Re: [AMBER] Error in prmtop and inpcrd atom
(Mon Jul 08 2019 - 00:34:23 PDT)
[AMBER] Error in prmtop and inpcrd atom
(Wed Jul 03 2019 - 10:06:19 PDT)
Sofia Vasilakaki
Re: [AMBER] Antechamber Charge Methods
(Mon Jul 01 2019 - 14:08:02 PDT)
[AMBER] Antechamber Charge Methods
(Mon Jul 01 2019 - 07:26:10 PDT)
somdev pahari
Re: [AMBER] Error in prmtop and inpcrd atom
(Mon Jul 08 2019 - 21:54:36 PDT)
Steven Ramsey
Re: [AMBER] question about GIST calculation
(Tue Jul 30 2019 - 07:39:01 PDT)
student_cbc_1 nnlab
[AMBER] Parameter file for GTP or GMP containing tRNA
(Sun Jul 21 2019 - 08:38:11 PDT)
Supriyo Bhattacharya
Re: [AMBER] Export command not found (export CUDA_VISIBLE_DEVICES)
(Mon Jul 08 2019 - 11:44:27 PDT)
Sérgio Marques
[AMBER] Help with parameters for iron centers
(Thu Jul 18 2019 - 05:00:39 PDT)
Thomas Evangelidis
[AMBER] PM6 charges for MD with AMBER
(Thu Jul 11 2019 - 02:52:34 PDT)
Tyler Luchko
Re: [AMBER] Compiling MPI 3D-RISM
(Wed Jul 10 2019 - 08:02:59 PDT)
Tyler Luchko (Lists)
Re: [AMBER] Thermodynamic information of RISM
(Mon Jul 01 2019 - 10:09:15 PDT)
Vaibhav Dixit
[AMBER] conformational sampling for organic/drug-like compounds
(Wed Jul 10 2019 - 11:16:12 PDT)
Violeta Burns Casamayor
Re: [AMBER] Error in prmtop and inpcrd atom
(Tue Jul 09 2019 - 06:20:53 PDT)
Re: [AMBER] changes in periodic box dimensions after pmemd.cuda run
(Mon Jul 01 2019 - 10:12:29 PDT)
Vishnudatt Pandey
[AMBER] To stop the message service
(Wed Jul 10 2019 - 03:57:29 PDT)
Vítor Felix
Re: [AMBER] How to replicate the number of lipids in bilayer for membrane dynamics
(Fri Jul 05 2019 - 02:02:29 PDT)
Xikun Liu
[AMBER] Can't load trajectory in coordinate formate from amber in VMD
(Tue Jul 23 2019 - 18:35:46 PDT)
Zachary Fallon
Re: [AMBER] How to generate topology file for protein-ATP complex
(Wed Jul 10 2019 - 09:54:24 PDT)
李耀
[AMBER] How to generate topology file for protein-ATP complex
(Wed Jul 10 2019 - 07:51:54 PDT)
谭畅
[AMBER] hbond
(Mon Jul 22 2019 - 08:45:37 PDT)
Re: [AMBER] electrostatic energy of mmgbsa decomposition
(Wed Jul 10 2019 - 04:06:37 PDT)
[AMBER] electrostatic energy of mmgbsa decomposition
(Wed Jul 10 2019 - 00:49:48 PDT)
[AMBER] problem about print_res
(Tue Jul 02 2019 - 18:15:52 PDT)
Last message date
:
Wed Jul 31 2019 - 13:30:03 PDT
Archived on
: Fri Dec 20 2024 - 05:55:52 PST
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