Amber Archive Jun 2019 by author
373 messages
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Starting
Fri May 31 2019 - 18:00:02 PDT,
Ending
Sun Jun 30 2019 - 12:30:02 PDT
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Abhilash J
[AMBER] Double metal ion parameterization using MCPB.py
(Tue Jun 04 2019 - 03:02:26 PDT)
accuratefreeenergy.gmail.com
Re: [AMBER] cuda 10.1 compile warnings
(Mon Jun 24 2019 - 10:23:27 PDT)
Aidan Reynolds
Re: [AMBER] tleap ERROR
(Mon Jun 03 2019 - 08:57:43 PDT)
Akinpelu Olayinka
[AMBER] Heating Error
(Mon Jun 24 2019 - 07:03:45 PDT)
[AMBER] Antechamber Error
(Fri Jun 14 2019 - 02:44:01 PDT)
Akshay Prabhakant
[AMBER] Extract potential energy of ligand
(Fri Jun 28 2019 - 11:51:29 PDT)
Albert
Re: [AMBER] problem of CUDA MPI
(Fri Jun 21 2019 - 08:27:52 PDT)
Re: [AMBER] problem of CUDA MPI
(Thu Jun 20 2019 - 05:39:53 PDT)
[AMBER] problem of CUDA MPI
(Thu Jun 20 2019 - 04:08:50 PDT)
Alen Ahmetovic
Re: [AMBER] mmpbsa/entropy frames
(Fri Jun 28 2019 - 13:27:37 PDT)
[AMBER] mmpbsa/entropy frames
(Thu Jun 27 2019 - 20:15:31 PDT)
Alessandro LANDI
Re: [AMBER] Problem with mol2 file generated by Antechamber
(Thu Jun 27 2019 - 07:24:24 PDT)
[AMBER] Problem with mol2 file generated by Antechamber
(Thu Jun 13 2019 - 07:51:10 PDT)
Andrew Bostick
[AMBER] stopping antechamber
(Fri Jun 28 2019 - 08:50:47 PDT)
Anthony Bogetti
[AMBER] Convergence issues in QM/MM simulations involving charge separation
(Tue Jun 04 2019 - 07:29:01 PDT)
Anuja Ware
Re: [AMBER] Using Gaussian 16 as external QM software with amber 14
(Tue Jun 18 2019 - 09:59:16 PDT)
[AMBER] Using Gaussian 16 as external QM software with amber 14
(Mon Jun 17 2019 - 04:08:01 PDT)
ARITRA MITRA
[AMBER] Insight into CMAP corrections
(Thu Jun 20 2019 - 22:40:53 PDT)
Barb, Adam [BBMBS]
[AMBER] Non-integer charge problem with tleap using GLYCAM_06EPb but not GLYCAM_06j-1
(Wed Jun 12 2019 - 07:12:03 PDT)
Bill Ross
[AMBER] leap chirally mirrored and flipped the first half of my weekend
(Sun Jun 30 2019 - 03:04:51 PDT)
Re: [AMBER] error in REMD on GPUs
(Mon Jun 24 2019 - 21:05:10 PDT)
Re: [AMBER] error in REMD on GPUs
(Mon Jun 24 2019 - 21:01:19 PDT)
Re: [AMBER] Problem in creating topology and coordinate files
(Mon Jun 17 2019 - 22:49:25 PDT)
Re: [AMBER] Problem in creating topology and coordinate files
(Mon Jun 17 2019 - 22:47:39 PDT)
Re: [AMBER] temperature not reaching target value in heating simulation
(Sun Jun 02 2019 - 05:06:35 PDT)
Re: [AMBER] temperature not reaching target value in heating simulation
(Sun Jun 02 2019 - 05:00:05 PDT)
Carlos Simmerling
Re: [AMBER] Amber mask for harmonic restraints
(Mon Jun 24 2019 - 04:18:26 PDT)
Re: [AMBER] Insight into CMAP corrections
(Fri Jun 21 2019 - 07:09:57 PDT)
Re: [AMBER] NaN Error
(Thu Jun 20 2019 - 08:31:11 PDT)
Re: [AMBER] NaN Error
(Thu Jun 20 2019 - 07:33:11 PDT)
Re: [AMBER] NaN Error
(Thu Jun 20 2019 - 07:15:14 PDT)
Re: [AMBER] NaN Error
(Thu Jun 20 2019 - 06:52:09 PDT)
Re: [AMBER] ff19SB forcefield
(Wed Jun 19 2019 - 10:27:07 PDT)
Re: [AMBER] Problem in creating topology and coordinate files
(Wed Jun 19 2019 - 04:35:19 PDT)
Re: [AMBER] ff14IDPs and ffIDPSFF
(Fri Jun 14 2019 - 06:50:54 PDT)
Re: [AMBER] Amber 18 licence
(Thu Jun 06 2019 - 05:27:40 PDT)
Charles-Alexandre Mattelaer
Re: [AMBER] Amplitude of ring puckering
(Mon Jun 17 2019 - 12:43:56 PDT)
[AMBER] Amplitude of ring puckering
(Sat Jun 15 2019 - 05:59:44 PDT)
[AMBER] Unit of pucker amplitude
(Fri Jun 14 2019 - 23:30:33 PDT)
Charu Sharma (JRF)
[AMBER] Fwd:
(Tue Jun 11 2019 - 11:10:19 PDT)
Chetna Tyagi
[AMBER] How can we simulate only the ligand-bound domain of the protein?
(Fri Jun 28 2019 - 05:15:59 PDT)
Re: [AMBER] counting water molecules through transmembrane pore
(Thu Jun 13 2019 - 01:32:42 PDT)
[AMBER] counting water molecules through transmembrane pore
(Wed Jun 12 2019 - 09:09:54 PDT)
Chris Neale
Re: [AMBER] changes in periodic box dimensions after pmemd.cuda run
(Fri Jun 28 2019 - 23:46:57 PDT)
cpimenta
[AMBER] CpHMD usage
(Fri Jun 07 2019 - 03:08:03 PDT)
Cruzeiro, Vinicius
Re: [AMBER] Correct procedure to perform CpHMD simulations
(Tue Jun 25 2019 - 10:35:18 PDT)
Cruzeiro,Vinicius Wilian D
Re: [AMBER] Constant pH simulation of PyroPhosphate in Explicit solvent
(Mon Jun 17 2019 - 10:52:03 PDT)
Re: [AMBER] CpHMD usage
(Fri Jun 07 2019 - 10:10:27 PDT)
Re: [AMBER] empty cein file redox potential calculations
(Mon Jun 03 2019 - 10:33:50 PDT)
Re: [AMBER] empty cein file redox potential calculations
(Mon Jun 03 2019 - 10:20:55 PDT)
Daniel Fernández Remacha
Re: [AMBER] [UCE] Re: DBSCAN CLUSTERING STARTS AT 0 CLUSTERS
(Thu Jun 13 2019 - 15:01:25 PDT)
Daniel Roe
Re: [AMBER] RMSF CPPTRAJ
(Thu Jun 27 2019 - 08:17:59 PDT)
Re: [AMBER] how to check if bad contacts exsist after min heat jobs
(Thu Jun 27 2019 - 08:14:44 PDT)
Re: [AMBER] Problem with mol2 file generated by Antechamber
(Thu Jun 27 2019 - 08:10:19 PDT)
Re: [AMBER] Pressure regulation with position restraints
(Mon Jun 24 2019 - 04:31:01 PDT)
Re: [AMBER] ambpdb hetatm connectivity only
(Sat Jun 22 2019 - 04:55:59 PDT)
Re: [AMBER] problem of CUDA MPI
(Fri Jun 21 2019 - 11:43:56 PDT)
Re: [AMBER] RMSF CPPTRAJ
(Thu Jun 20 2019 - 05:41:34 PDT)
Re: [AMBER] hbond
(Wed Jun 19 2019 - 03:24:56 PDT)
Re: [AMBER] Fw: parameterization of ligand+protein complex
(Tue Jun 18 2019 - 09:31:56 PDT)
Re: [AMBER] [UCE] Re: DBSCAN CLUSTERING STARTS AT 0 CLUSTERS
(Tue Jun 18 2019 - 09:19:20 PDT)
Re: [AMBER] Amplitude of ring puckering
(Tue Jun 18 2019 - 09:13:25 PDT)
Re: [AMBER] Fw: parameterization of ligand+protein complex
(Tue Jun 18 2019 - 09:10:29 PDT)
Re: [AMBER] The membran-water system ran out of the box
(Tue Jun 18 2019 - 09:09:28 PDT)
Re: [AMBER] Amplitude of ring puckering
(Mon Jun 17 2019 - 12:41:23 PDT)
Re: [AMBER] RMSF phi angle
(Fri Jun 14 2019 - 11:26:27 PDT)
Re: [AMBER] [UCE] Re: DBSCAN CLUSTERING STARTS AT 0 CLUSTERS
(Fri Jun 14 2019 - 06:46:27 PDT)
Re: [AMBER] hbond
(Thu Jun 13 2019 - 16:26:16 PDT)
Re: [AMBER] Problems using stfcdiffusion
(Thu Jun 13 2019 - 12:53:52 PDT)
Re: [AMBER] [UCE] Re: DBSCAN CLUSTERING STARTS AT 0 CLUSTERS
(Thu Jun 13 2019 - 12:49:45 PDT)
Re: [AMBER] DBSCAN CLUSTERING STARTS AT 0 CLUSTERS
(Thu Jun 13 2019 - 12:12:00 PDT)
Re: [AMBER] hbond
(Thu Jun 13 2019 - 10:57:59 PDT)
Re: [AMBER] hbond
(Thu Jun 13 2019 - 08:55:07 PDT)
Re: [AMBER] cpptraj hbond calculation
(Thu Jun 13 2019 - 06:43:55 PDT)
Re: [AMBER] cpptraj hbond calculation
(Wed Jun 12 2019 - 10:22:22 PDT)
Re: [AMBER] cpptraj hbond between ligand protein/wat
(Mon Jun 10 2019 - 05:32:29 PDT)
Re: [AMBER] Write out box dimensions in the trajectory
(Tue Jun 04 2019 - 11:56:52 PDT)
Re: [AMBER] Cpptraj RMSF
(Tue Jun 04 2019 - 10:29:15 PDT)
David A Case
Re: [AMBER] Issue installing Amber18 pbsa.cuda
(Tue Jun 25 2019 - 05:04:16 PDT)
Re: [AMBER] What is the effect of 150mM of salt in simulations?
(Mon Jun 24 2019 - 12:12:44 PDT)
Re: [AMBER] Heating Error
(Mon Jun 24 2019 - 08:39:19 PDT)
Re: [AMBER] Pressure regulation with position restraints
(Mon Jun 24 2019 - 05:24:22 PDT)
Re: [AMBER] Issue installing Amber18 pbsa.cuda
(Mon Jun 24 2019 - 05:18:14 PDT)
Re: [AMBER] Amber mask for harmonic restraints
(Mon Jun 24 2019 - 05:12:07 PDT)
Re: [AMBER] qmmm error
(Mon Jun 17 2019 - 04:56:56 PDT)
Re: [AMBER] Antechamber Error
(Fri Jun 14 2019 - 04:51:45 PDT)
Re: [AMBER] Fw: Ligand Parameterization
(Thu Jun 13 2019 - 09:29:54 PDT)
Re: [AMBER] Amber installation error
(Thu Jun 13 2019 - 09:25:54 PDT)
Re: [AMBER] Installing amber with CUDA as local user on supercomputer
(Thu Jun 13 2019 - 09:20:12 PDT)
Re: [AMBER] [Amber]-help-messy rst output using Sander
(Thu Jun 13 2019 - 05:00:27 PDT)
Re: [AMBER] Tleap impose command for boron
(Wed Jun 12 2019 - 09:57:15 PDT)
Re: [AMBER] I have a problem in using LEaP.
(Wed Jun 12 2019 - 04:35:47 PDT)
Re: [AMBER] Convergence issues in QM/MM simulations involving charge separation
(Fri Jun 07 2019 - 11:24:50 PDT)
Re: [AMBER] Regular Ewald calculations on GPU
(Fri Jun 07 2019 - 11:19:45 PDT)
Re: [AMBER] Most recent GAFF version to use?
(Thu Jun 06 2019 - 06:55:34 PDT)
Re: [AMBER] tleap ERROR
(Tue Jun 04 2019 - 12:31:07 PDT)
Re: [AMBER] AMBER to RCSB pdb format for analysis in other tools like LeView
(Tue Jun 04 2019 - 05:11:39 PDT)
Re: [AMBER] temperature not reaching target value in heating simulation
(Tue Jun 04 2019 - 05:05:30 PDT)
Re: [AMBER] tleap ERROR
(Mon Jun 03 2019 - 09:06:21 PDT)
Re: [AMBER] Ab initio MD in AMBER
(Mon Jun 03 2019 - 09:04:33 PDT)
Re: [AMBER] temperature not reaching target value in heating simulation
(Mon Jun 03 2019 - 08:59:26 PDT)
Re: [AMBER] Error analysis of a trajetory
(Mon Jun 03 2019 - 05:03:39 PDT)
Re: [AMBER] temperature not reaching target value in heating simulation
(Mon Jun 03 2019 - 04:58:06 PDT)
David Case
Re: [AMBER] How can we simulate only the ligand-bound domain of the protein?
(Sun Jun 30 2019 - 05:32:31 PDT)
Re: [AMBER] Error: "System must be very inhomogeneous"
(Sun Jun 30 2019 - 05:28:02 PDT)
Re: [AMBER] mmpbsa/entropy frames
(Fri Jun 28 2019 - 05:37:57 PDT)
Re: [AMBER] Program received signal SIGSEGV: Segmentation fault - invalid memory reference. error
(Fri Jun 28 2019 - 05:27:07 PDT)
Re: [AMBER] RESTARTED DUE TO LINMIN FAILURE
(Fri Jun 28 2019 - 05:24:07 PDT)
Re: [AMBER] RESTARTED DUE TO LINMIN FAILURE
(Thu Jun 27 2019 - 13:01:09 PDT)
Re: [AMBER] how to check if bad contacts exsist after min heat jobs
(Wed Jun 26 2019 - 19:11:11 PDT)
Re: [AMBER] Problem in creating topology and coordinate files
(Mon Jun 24 2019 - 19:03:50 PDT)
Re: [AMBER] open valance problem
(Mon Jun 24 2019 - 18:59:20 PDT)
Re: [AMBER] GAFF2 Missing parameters -
(Sun Jun 23 2019 - 06:12:34 PDT)
Re: [AMBER] Antechamber (sqm) charge generation
(Sun Jun 23 2019 - 06:05:54 PDT)
Re: [AMBER] framed parameters
(Thu Jun 20 2019 - 07:01:40 PDT)
Re: [AMBER] Fw: parameterization of ligand+protein complex
(Thu Jun 20 2019 - 06:37:06 PDT)
Re: [AMBER] problem of CUDA MPI
(Wed Jun 19 2019 - 22:48:53 PDT)
Re: [AMBER] Adding disulphide bonds.
(Wed Jun 19 2019 - 09:10:43 PDT)
Re: [AMBER] solvateoct and sovlatebox errors while solvating ligand
(Sun Jun 16 2019 - 06:13:24 PDT)
Re: [AMBER] File missing in the apr tutorial
(Sat Jun 15 2019 - 05:56:13 PDT)
Re: [AMBER] Problem with mol2 file generated by Antechamber
(Sat Jun 15 2019 - 05:51:31 PDT)
Re: [AMBER] Atom type for fluorine atom in glycam force field -reg.
(Tue Jun 11 2019 - 08:30:35 PDT)
Re: [AMBER] error with loading HEM parameters for constph redox calcuations
(Fri May 31 2019 - 17:57:39 PDT)
David Cerutti
Re: [AMBER] Modeling of flexible enzyme: on the selection of the thermostat
(Thu Jun 27 2019 - 08:34:24 PDT)
Re: [AMBER] ntt=9 in pmemd?
(Wed Jun 26 2019 - 18:45:24 PDT)
Re: [AMBER] ntt=9 in pmemd?
(Wed Jun 26 2019 - 13:15:52 PDT)
Re: [AMBER] Modeling of flexible enzyme: on the selection of the thermostat
(Wed Jun 26 2019 - 12:09:07 PDT)
Re: [AMBER] Modeling of flexible enzyme: on the selection of the thermostat
(Tue Jun 25 2019 - 11:51:15 PDT)
Re: [AMBER] What is the effect of 150mM of salt in simulations?
(Mon Jun 24 2019 - 12:07:20 PDT)
Re: [AMBER] [Amber]-help-messy rst output using Sander
(Wed Jun 12 2019 - 12:35:29 PDT)
Re: [AMBER] Fwd:
(Tue Jun 11 2019 - 11:18:40 PDT)
David Slochower
Re: [AMBER] File missing in the apr tutorial
(Wed Jun 19 2019 - 11:26:34 PDT)
Debarati DasGupta
[AMBER] SPAM calculations in cpptraj
(Tue Jun 25 2019 - 06:32:13 PDT)
dnlfr1994.gmail.com
Re: [AMBER] [UCE] Re: DBSCAN CLUSTERING STARTS AT 0 CLUSTERS
(Mon Jun 17 2019 - 04:43:06 PDT)
[AMBER] DBSCAN CLUSTERING STARTS AT 0 CLUSTERS
(Thu Jun 13 2019 - 10:04:33 PDT)
Elvis Martis
Re: [AMBER] RESTARTED DUE TO LINMIN FAILURE
(Thu Jun 27 2019 - 09:23:53 PDT)
Re: [AMBER] open valance problem
(Wed Jun 26 2019 - 22:02:44 PDT)
Re: [AMBER] open valance problem
(Tue Jun 25 2019 - 21:53:03 PDT)
Re: [AMBER] open valance problem
(Mon Jun 24 2019 - 22:11:29 PDT)
Re: [AMBER] open valance problem
(Sat Jun 22 2019 - 20:56:57 PDT)
Re: [AMBER] Antechamber Error
(Fri Jun 14 2019 - 04:13:21 PDT)
Re: [AMBER] bash: leaprc.protein.ff14SB: No such file or directory
(Thu Jun 13 2019 - 23:40:07 PDT)
emanuele falbo
[AMBER] convert AMBER files to CHARMM
(Thu Jun 06 2019 - 06:06:36 PDT)
Erdem Yeler
[AMBER] Tleap impose command for boron
(Wed Jun 12 2019 - 08:21:38 PDT)
[AMBER] How to Calculate Frequency Analysis and Intermolecular Energies by Using Amber
(Wed Jun 05 2019 - 14:59:21 PDT)
[AMBER] Paramfit non-gaff atom problem
(Sun Jun 02 2019 - 08:22:06 PDT)
Fabian Glaser
[AMBER] cyclen derived copper ligand parametrisation
(Mon Jun 24 2019 - 05:11:27 PDT)
[AMBER] framed parameters
(Thu Jun 20 2019 - 05:41:26 PDT)
[AMBER] CU library file
(Thu Jun 13 2019 - 08:09:25 PDT)
Re: [AMBER] phosphor tyrosine bound to C5' terminal DA5
(Sun Jun 02 2019 - 06:21:58 PDT)
Fotis Baltoumas
[AMBER] "Official" / valid Amber-GAFF parameters for 1-octanol
(Thu Jun 13 2019 - 09:45:54 PDT)
Francesca Lønstad Bleken
Re: [AMBER] QMMM, with NWChem and Amber
(Wed Jun 19 2019 - 00:21:07 PDT)
[AMBER] QMMM, with NWChem and Amber
(Tue Jun 18 2019 - 05:04:28 PDT)
[AMBER] Installing amber with CUDA as local user on supercomputer
(Thu Jun 13 2019 - 04:55:30 PDT)
Franz Waibl
Re: [AMBER] Pressure regulation with position restraints
(Mon Jun 24 2019 - 11:45:08 PDT)
Re: [AMBER] Pressure regulation with position restraints
(Mon Jun 24 2019 - 11:07:18 PDT)
Re: [AMBER] Pressure regulation with position restraints
(Mon Jun 24 2019 - 07:13:02 PDT)
[AMBER] Pressure regulation with position restraints
(Mon Jun 24 2019 - 04:07:33 PDT)
Gerardo Zerbetto De Palma
Re: [AMBER] tleap ERROR
(Mon Jun 03 2019 - 10:32:56 PDT)
Re: [AMBER] tleap ERROR
(Mon Jun 03 2019 - 10:31:18 PDT)
Re: [AMBER] tleap ERROR
(Mon Jun 03 2019 - 08:54:51 PDT)
Gert Kruger
Re: [AMBER] Using Gaussian 16 as external QM software with amber 14
(Mon Jun 17 2019 - 23:19:54 PDT)
Re: [AMBER] bash: leaprc.protein.ff14SB: No such file or directory
(Fri Jun 14 2019 - 03:11:23 PDT)
[AMBER] bash: leaprc.protein.ff14SB: No such file or directory
(Thu Jun 13 2019 - 23:17:15 PDT)
Gustaf Olsson
Re: [AMBER] Error: "System must be very inhomogeneous"
(Sat Jun 29 2019 - 23:43:34 PDT)
Re: [AMBER] I have a problem in using LEaP.
(Wed Jun 12 2019 - 07:07:51 PDT)
Re: [AMBER] I have a problem in using LEaP.
(Tue Jun 11 2019 - 21:53:49 PDT)
hii
[AMBER] Dealing with non standard amino acid
(Fri May 31 2019 - 22:03:20 PDT)
Hira Jabeen
Re: [AMBER] Fw: parameterization of ligand+protein complex
(Thu Jun 20 2019 - 04:04:27 PDT)
Re: [AMBER] Fw: parameterization of ligand+protein complex
(Thu Jun 20 2019 - 03:54:49 PDT)
Re: [AMBER] Fw: parameterization of ligand+protein complex
(Wed Jun 19 2019 - 04:20:19 PDT)
Re: [AMBER] Fw: parameterization of ligand+protein complex
(Tue Jun 18 2019 - 09:13:58 PDT)
[AMBER] Fw: parameterization of ligand+protein complex
(Tue Jun 18 2019 - 03:27:53 PDT)
[AMBER] parameterization of ligand+protein complex
(Fri Jun 14 2019 - 09:09:45 PDT)
[AMBER] Fw: Ligand Parameterization
(Thu Jun 13 2019 - 05:53:14 PDT)
Hosein Geraili Daronkola
[AMBER] Loop of H1-H2 in ZN6 of ZAFF
(Mon Jun 17 2019 - 09:10:56 PDT)
Hossein Pourreza
Re: [AMBER] multi gpu run using MPI
(Tue Jun 11 2019 - 06:12:33 PDT)
[AMBER] multi gpu run using MPI
(Thu Jun 06 2019 - 13:35:20 PDT)
Jacob Monroe
Re: [AMBER] Pressure regulation with position restraints
(Mon Jun 24 2019 - 11:20:53 PDT)
Re: [AMBER] Pressure regulation with position restraints
(Mon Jun 24 2019 - 08:13:02 PDT)
jacob wick
Re: [AMBER] Correct procedure to perform CpHMD simulations
(Wed Jun 26 2019 - 03:28:09 PDT)
[AMBER] Correct procedure to perform CpHMD simulations
(Tue Jun 25 2019 - 06:56:36 PDT)
James Kress
Re: [AMBER] QMMM, with NWChem and Amber
(Tue Jun 18 2019 - 09:50:15 PDT)
James Starlight
Re: [AMBER] Modeling of flexible enzyme: on the selection of the thermostat
(Thu Jun 27 2019 - 01:18:14 PDT)
Re: [AMBER] Modeling of flexible enzyme: on the selection of the thermostat
(Tue Jun 25 2019 - 23:39:33 PDT)
[AMBER] Modeling of flexible enzyme: on the selection of the thermostat
(Tue Jun 25 2019 - 11:20:29 PDT)
Re: [AMBER] Amber mask for harmonic restraints
(Mon Jun 24 2019 - 05:39:43 PDT)
[AMBER] Amber mask for harmonic restraints
(Sun Jun 23 2019 - 11:49:27 PDT)
Jeyaram R A
Re: [AMBER] Atom type for fluorine atom in glycam force field -reg.
(Tue Jun 11 2019 - 21:45:28 PDT)
[AMBER] Atom type for fluorine atom in glycam force field -reg.
(Tue Jun 11 2019 - 05:39:49 PDT)
[AMBER] substitution of fluorine atom at o9 hydroxyl group sialic acid by using glycam force field -reg
(Sun Jun 09 2019 - 22:30:32 PDT)
Joan Torras
Re: [AMBER] QMMM, with NWChem and Amber
(Wed Jun 19 2019 - 06:52:55 PDT)
Josh Berryman
Re: [AMBER] NaN Error
(Thu Jun 20 2019 - 11:06:51 PDT)
Re: [AMBER] NaN Error
(Thu Jun 20 2019 - 08:16:26 PDT)
Re: [AMBER] NaN Error
(Thu Jun 20 2019 - 07:28:41 PDT)
Keiran Corbett
[AMBER] Error analysis of a trajetory
(Sun Jun 02 2019 - 07:00:26 PDT)
Kenneth Huang
Re: [AMBER] ntt=9 in pmemd?
(Wed Jun 26 2019 - 14:08:42 PDT)
[AMBER] ntt=9 in pmemd?
(Wed Jun 26 2019 - 13:07:04 PDT)
Lod King
Re: [AMBER] RMSF CPPTRAJ
(Wed Jun 26 2019 - 18:46:18 PDT)
Re: [AMBER] RMSF phi angle
(Fri Jun 14 2019 - 11:41:39 PDT)
[AMBER] RMSF CPPTRAJ
(Fri Jun 14 2019 - 09:59:04 PDT)
[AMBER] RMSF phi angle
(Fri Jun 14 2019 - 09:24:18 PDT)
[AMBER] ff14IDPs and ffIDPSFF
(Tue Jun 11 2019 - 01:12:55 PDT)
[AMBER] Cpptraj RMSF
(Tue Jun 04 2019 - 10:10:49 PDT)
Luca Codutti
[AMBER] cuda 10.1 compile warnings
(Mon Jun 24 2019 - 09:19:52 PDT)
Lucas Bandeira
[AMBER] Error: "System must be very inhomogeneous"
(Sat Jun 29 2019 - 09:59:13 PDT)
[AMBER] Problems with iwrap
(Wed Jun 26 2019 - 11:26:26 PDT)
[AMBER] Problems using stfcdiffusion
(Fri Jun 14 2019 - 11:22:19 PDT)
Re: [AMBER] Problems using stfcdiffusion
(Fri Jun 14 2019 - 09:32:21 PDT)
[AMBER] Problems using stfcdiffusion
(Thu Jun 13 2019 - 11:27:07 PDT)
Lutimba-Stuart
[AMBER] Description of atom types for Ergosterol
(Mon Jun 17 2019 - 12:13:34 PDT)
M RCC
[AMBER] What is the effect of 150mM of salt in simulations?
(Mon Jun 24 2019 - 11:38:50 PDT)
Mahesh kumar Teli
Re: [AMBER] Issue installing Amber18 pbsa.cuda
(Mon Jun 24 2019 - 20:03:10 PDT)
[AMBER] Issue installing Amber18 cuda
(Mon Jun 24 2019 - 02:09:31 PDT)
Marawan Hussien
[AMBER] Immediate postdoc opening in Bio-molecular simulation, University of Alberta, Canada
(Wed Jun 19 2019 - 17:17:19 PDT)
Marcela Madrid
Re: [AMBER] error in REMD on GPUs
(Tue Jun 25 2019 - 06:31:59 PDT)
[AMBER] error in REMD on GPUs
(Mon Jun 24 2019 - 20:36:11 PDT)
Marcos Serrou do Amaral
Re: [AMBER] Costant ph simulation for Small molecules
(Fri Jun 07 2019 - 03:31:12 PDT)
Margarita I. Bernal-Uruchurtu
[AMBER] Quantum mechanical models for proton transfer studies in AMBER
(Wed Jun 05 2019 - 02:27:50 PDT)
Markowska
Re: [AMBER] counting water molecules through transmembrane pore
(Wed Jun 12 2019 - 13:40:04 PDT)
Maryam
[AMBER] external electric field
(Fri Jun 21 2019 - 09:22:47 PDT)
Matias Machado
Re: [AMBER] Problem with mol2 file generated by Antechamber
(Thu Jun 27 2019 - 08:04:28 PDT)
Re: [AMBER] how to check if bad contacts exsist after min heat jobs
(Wed Jun 26 2019 - 11:40:39 PDT)
Re: [AMBER] Modeling of flexible enzyme: on the selection of the thermostat
(Wed Jun 26 2019 - 10:54:33 PDT)
Re: [AMBER] ff19SB forcefield
(Wed Jun 19 2019 - 09:35:11 PDT)
Re: [AMBER] Fw: parameterization of ligand+protein complex
(Wed Jun 19 2019 - 07:36:34 PDT)
Re: [AMBER] Problem with mol2 file generated by Antechamber
(Thu Jun 13 2019 - 09:02:35 PDT)
Re: [AMBER] CU library file
(Thu Jun 13 2019 - 08:38:30 PDT)
Re: [AMBER] Urea water mixture
(Tue Jun 11 2019 - 08:54:06 PDT)
Re: [AMBER] propka web server
(Sat Jun 08 2019 - 13:30:47 PDT)
Re: [AMBER] Most recent GAFF version to use?
(Fri Jun 07 2019 - 13:12:51 PDT)
Re: [AMBER] propka web server
(Fri Jun 07 2019 - 10:29:31 PDT)
Re: [AMBER] Most recent GAFF version to use?
(Thu Jun 06 2019 - 08:50:28 PDT)
Re: [AMBER] tleap ERROR
(Tue Jun 04 2019 - 09:11:42 PDT)
Re: [AMBER] error with loading HEM parameters for constph redox calcuations
(Mon Jun 03 2019 - 16:10:13 PDT)
Re: [AMBER] tleap ERROR
(Mon Jun 03 2019 - 15:27:19 PDT)
Maximilien BERNE
Re: [AMBER] Some errors for the membrane system
(Mon Jun 03 2019 - 02:28:05 PDT)
Melania T
Re: [AMBER] Antechamber (sqm) charge generation
(Sun Jun 23 2019 - 12:13:17 PDT)
Re: [AMBER] GAFF2 Missing parameters -
(Sun Jun 23 2019 - 10:23:01 PDT)
Re: [AMBER] Antechamber (sqm) charge generation
(Sun Jun 23 2019 - 10:15:48 PDT)
[AMBER] Antechamber (sqm) charge generation
(Fri Jun 21 2019 - 23:46:25 PDT)
[AMBER] GAFF2 Missing parameters -
(Fri Jun 21 2019 - 23:05:57 PDT)
Re: [AMBER] Most recent GAFF version to use?
(Thu Jun 06 2019 - 22:54:37 PDT)
[AMBER] Most recent GAFF version to use?
(Wed Jun 05 2019 - 14:17:18 PDT)
Mohammad Hassan Khatami
[AMBER] Adding inhomogeneous force
(Thu Jun 27 2019 - 10:59:40 PDT)
Mohammed I Sorour
[AMBER] Gromacs-4.6 to Amber Parameter Conversion
(Sun Jun 09 2019 - 16:03:05 PDT)
MOHD HOMAIDUR RAHMAN
[AMBER] Higher level spline correction to PMF obtain from low-level QM/MM umbrella impelling
(Tue Jun 11 2019 - 08:44:11 PDT)
Mustafa Alhaji Isa
[AMBER] Problem in creating topology and coordinate files
(Mon Jun 17 2019 - 22:45:20 PDT)
Niel Henriksen
Re: [AMBER] Most recent GAFF version to use?
(Fri Jun 07 2019 - 12:01:49 PDT)
Nikolay N. Kuzmich
[AMBER] ff19SB forcefield
(Wed Jun 19 2019 - 01:46:39 PDT)
Re: [AMBER] Regular Ewald calculations on GPU
(Sat Jun 08 2019 - 07:26:36 PDT)
[AMBER] Regular Ewald calculations on GPU
(Fri Jun 07 2019 - 10:35:33 PDT)
Re: [AMBER] Ab initio MD in AMBER
(Wed Jun 05 2019 - 05:10:39 PDT)
Re: [AMBER] Ab initio MD in AMBER
(Tue Jun 04 2019 - 05:45:37 PDT)
[AMBER] Ab initio MD in AMBER
(Mon Jun 03 2019 - 06:19:01 PDT)
Nisha Amarnath Jonniya
Re: [AMBER] Amber installation error
(Fri Jun 14 2019 - 04:38:01 PDT)
[AMBER] Amber installation error
(Thu Jun 13 2019 - 05:06:29 PDT)
Nora Kremer
Re: [AMBER] Urea water mixture
(Wed Jun 12 2019 - 07:13:58 PDT)
[AMBER] Urea water mixture
(Tue Jun 11 2019 - 07:16:25 PDT)
Paula Mihaljevic-Juric
Re: [AMBER] NaN Error
(Thu Jun 20 2019 - 08:28:41 PDT)
Re: [AMBER] NaN Error
(Thu Jun 20 2019 - 08:00:11 PDT)
Re: [AMBER] NaN Error
(Thu Jun 20 2019 - 07:20:52 PDT)
Re: [AMBER] NaN Error
(Thu Jun 20 2019 - 07:09:26 PDT)
[AMBER] NaN Error
(Thu Jun 20 2019 - 06:34:50 PDT)
Pengfei Li
Re: [AMBER] Loop of H1-H2 in ZN6 of ZAFF
(Thu Jun 20 2019 - 13:44:42 PDT)
Re: [AMBER] Double metal ion parameterization using MCPB.py
(Sat Jun 15 2019 - 17:57:07 PDT)
Re: [AMBER] deselect residues for step1 model in MCPB.py
(Sat Jun 01 2019 - 12:33:12 PDT)
Re: [AMBER] Error in step 3 of MCPB.py
(Sat Jun 01 2019 - 12:27:26 PDT)
Prashanth Athri
[AMBER] Dihedral parameters in a small molecule
(Sun Jun 23 2019 - 18:18:18 PDT)
Pratul Agarwal
Re: [AMBER] Ab initio MD in AMBER
(Wed Jun 05 2019 - 08:32:32 PDT)
Re: [AMBER] Ab initio MD in AMBER
(Tue Jun 04 2019 - 06:03:46 PDT)
Rajarshi Roy
[AMBER] Regarding nmode error
(Sun Jun 30 2019 - 07:24:31 PDT)
Ray Luo
Re: [AMBER] Issue installing Amber18 pbsa.cuda
(Tue Jun 25 2019 - 05:51:18 PDT)
Re: [AMBER] MMPBSA radiopt effect on EDISPER
(Mon Jun 24 2019 - 14:23:14 PDT)
Re: [AMBER] MMPBSA radiopt effect on EDISPER
(Wed Jun 19 2019 - 15:54:28 PDT)
Re: [AMBER] MMPBSA radiopt effect on EDISPER
(Wed Jun 19 2019 - 14:14:11 PDT)
Re: [AMBER] MMPBSA radiopt effect on EDISPER
(Wed Jun 19 2019 - 07:51:24 PDT)
Re: [AMBER] MMPBSA radiopt effect on EDISPER
(Mon Jun 17 2019 - 16:20:12 PDT)
Rodriguez, Yoel
[AMBER] MD Simulation in DMSO
(Mon Jun 24 2019 - 05:11:53 PDT)
Ross Walker
Re: [AMBER] Recommended CUDA version for Amber18-19 on RTX GPUs?
(Sun Jun 23 2019 - 16:21:54 PDT)
Re: [AMBER] Installing amber with CUDA as local user on supercomputer
(Thu Jun 13 2019 - 07:42:51 PDT)
Re: [AMBER] multi gpu run using MPI
(Tue Jun 11 2019 - 06:10:30 PDT)
Rui Chen
Re: [AMBER] Adding disulphide bonds.
(Wed Jun 19 2019 - 14:22:52 PDT)
[AMBER] Adding disulphide bonds.
(Tue Jun 18 2019 - 16:21:43 PDT)
Re: [AMBER] I have a problem in using LEaP.
(Wed Jun 12 2019 - 08:30:09 PDT)
Re: [AMBER] I have a problem in using LEaP.
(Wed Jun 12 2019 - 06:12:08 PDT)
Re: [AMBER] I have a problem in using LEaP.
(Wed Jun 12 2019 - 05:54:14 PDT)
Re: [AMBER] I have a problem in using LEaP.
(Tue Jun 11 2019 - 19:57:48 PDT)
[AMBER] I have a problem in using LEaP.
(Tue Jun 11 2019 - 18:24:45 PDT)
Sadaf Rani
[AMBER] Program received signal SIGSEGV: Segmentation fault - invalid memory reference. error
(Thu Jun 27 2019 - 12:09:22 PDT)
Re: [AMBER] RESTARTED DUE TO LINMIN FAILURE
(Thu Jun 27 2019 - 10:58:50 PDT)
[AMBER] RESTARTED DUE TO LINMIN FAILURE
(Thu Jun 27 2019 - 08:56:55 PDT)
Re: [AMBER] open valance problem
(Wed Jun 26 2019 - 14:30:53 PDT)
Re: [AMBER] open valance problem
(Tue Jun 25 2019 - 09:29:33 PDT)
Re: [AMBER] open valance problem
(Tue Jun 25 2019 - 07:34:51 PDT)
Re: [AMBER] open valance problem
(Tue Jun 25 2019 - 06:47:31 PDT)
Re: [AMBER] open valance problem
(Mon Jun 24 2019 - 13:25:51 PDT)
Re: [AMBER] sqm.pdb structure
(Mon Jun 24 2019 - 01:59:19 PDT)
Re: [AMBER] sqm.pdb structure
(Sat Jun 22 2019 - 08:35:50 PDT)
[AMBER] sqm.pdb structure
(Sat Jun 22 2019 - 07:24:59 PDT)
[AMBER] open valance problem
(Sat Jun 22 2019 - 06:26:25 PDT)
Re: [AMBER] propka web server
(Sat Jun 08 2019 - 05:27:11 PDT)
[AMBER] propka web server
(Fri Jun 07 2019 - 10:17:55 PDT)
Re: [AMBER] Amber 18 licence
(Thu Jun 06 2019 - 14:40:40 PDT)
[AMBER] Amber 18 licence
(Thu Jun 06 2019 - 05:01:57 PDT)
Re: [AMBER] tleap ERROR
(Tue Jun 04 2019 - 05:15:01 PDT)
Re: [AMBER] Question about sander running parallel
(Tue Jun 04 2019 - 02:53:09 PDT)
Re: [AMBER] tleap ERROR
(Mon Jun 03 2019 - 10:19:45 PDT)
[AMBER] tleap ERROR
(Mon Jun 03 2019 - 07:24:51 PDT)
Sina
[AMBER] qmmm error
(Sun Jun 16 2019 - 08:01:05 PDT)
somdev pahari
Re: [AMBER] hbond
(Thu Jun 13 2019 - 23:04:51 PDT)
Re: [AMBER] hbond
(Thu Jun 13 2019 - 16:50:59 PDT)
Re: [AMBER] hbond
(Thu Jun 13 2019 - 10:41:47 PDT)
Re: [AMBER] hbond
(Thu Jun 13 2019 - 21:56:45 PDT)
[AMBER] hbond
(Thu Jun 13 2019 - 07:39:32 PDT)
sribone.fcq.unc.edu.ar
Re: [AMBER] Problem with mol2 file generated by Antechamber
(Thu Jun 13 2019 - 08:35:38 PDT)
Stefano Motta
Re: [AMBER] hbond
(Thu Jun 13 2019 - 08:32:31 PDT)
[AMBER] cpptraj hbond calculation
(Wed Jun 12 2019 - 09:14:09 PDT)
[AMBER] Costant ph simulation for Small molecules
(Fri Jun 07 2019 - 02:22:23 PDT)
Stephan Schott
Re: [AMBER] Atom type for fluorine atom in glycam force field -reg.
(Tue Jun 11 2019 - 09:32:52 PDT)
Re: [AMBER] Atom type for fluorine atom in glycam force field -reg.
(Tue Jun 11 2019 - 06:33:45 PDT)
Steven M. Graham
Re: [AMBER] Amplitude of ring puckering
(Mon Jun 17 2019 - 12:48:07 PDT)
sunyeping
Re: [AMBER] parameter file for dUTP
(Tue Jun 04 2019 - 12:51:29 PDT)
Supriyo Bhattacharya
Re: [AMBER] How can we simulate only the ligand-bound domain of the protein?
(Sun Jun 30 2019 - 12:04:52 PDT)
Re: [AMBER] How can we simulate only the ligand-bound domain of the protein?
(Sun Jun 30 2019 - 11:43:41 PDT)
[AMBER] AMD with GB solvation
(Tue Jun 11 2019 - 12:08:33 PDT)
Thakur, Abhishek
Re: [AMBER] MM-PBSA
(Tue Jun 18 2019 - 11:31:45 PDT)
[AMBER] MM-PBSA
(Tue Jun 18 2019 - 11:09:07 PDT)
Thomas Cheatham
Re: [AMBER] Problems with iwrap
(Wed Jun 26 2019 - 16:14:45 PDT)
Re: [AMBER] NaN Error
(Thu Jun 20 2019 - 09:28:02 PDT)
Re: [AMBER] [UCE] Re: DBSCAN CLUSTERING STARTS AT 0 CLUSTERS
(Thu Jun 13 2019 - 12:45:45 PDT)
Thomas Gaillard
Re: [AMBER] MMPBSA radiopt effect on EDISPER
(Mon Jun 24 2019 - 03:46:15 PDT)
Re: [AMBER] MMPBSA radiopt effect on EDISPER
(Wed Jun 19 2019 - 15:34:50 PDT)
Re: [AMBER] MMPBSA radiopt effect on EDISPER
(Wed Jun 19 2019 - 07:49:20 PDT)
[AMBER] incorrect dispersion term when radiopt=0: bug found and solved
(Mon Jun 17 2019 - 06:18:27 PDT)
Re: [AMBER] MMPBSA radiopt effect on EDISPER
(Tue Jun 11 2019 - 06:49:08 PDT)
Vaibhav Dixit
Re: [AMBER] how to check if bad contacts exsist after min heat jobs
(Thu Jun 27 2019 - 08:46:46 PDT)
Re: [AMBER] how to check if bad contacts exsist after min heat jobs
(Thu Jun 27 2019 - 07:32:26 PDT)
Re: [AMBER] how to check if bad contacts exsist after min heat jobs
(Thu Jun 27 2019 - 01:11:16 PDT)
[AMBER] how to check if bad contacts exsist after min heat jobs
(Wed Jun 26 2019 - 07:48:24 PDT)
Re: [AMBER] ambpdb hetatm connectivity only
(Sat Jun 22 2019 - 07:05:57 PDT)
[AMBER] ambpdb hetatm connectivity only
(Sat Jun 22 2019 - 03:28:54 PDT)
Re: [AMBER] AMBER to RCSB pdb format for analysis in other tools like LeView
(Wed Jun 19 2019 - 14:42:25 PDT)
Re: [AMBER] AMBER to RCSB pdb format for analysis in other tools like LeView
(Wed Jun 19 2019 - 06:11:48 PDT)
Re: [AMBER] solvateoct and sovlatebox errors while solvating ligand
(Sun Jun 16 2019 - 09:46:47 PDT)
[AMBER] solvateoct and sovlatebox errors while solvating ligand
(Sun Jun 16 2019 - 01:47:28 PDT)
[AMBER] cpptraj hbond between ligand protein/wat
(Sat Jun 08 2019 - 05:24:37 PDT)
Re: [AMBER] AMBER to RCSB pdb format for analysis in other tools like LeView
(Tue Jun 04 2019 - 06:12:24 PDT)
[AMBER] AMBER to RCSB pdb format for analysis in other tools like LeView
(Tue Jun 04 2019 - 03:00:27 PDT)
Re: [AMBER] temperature not reaching target value in heating simulation
(Mon Jun 03 2019 - 11:27:12 PDT)
Re: [AMBER] empty cein file redox potential calculations
(Mon Jun 03 2019 - 10:23:34 PDT)
Re: [AMBER] tleap ERROR
(Mon Jun 03 2019 - 10:30:09 PDT)
Re: [AMBER] empty cein file redox potential calculations
(Mon Jun 03 2019 - 09:08:58 PDT)
Re: [AMBER] temperature not reaching target value in heating simulation
(Mon Jun 03 2019 - 05:22:23 PDT)
Re: [AMBER] temperature not reaching target value in heating simulation
(Sun Jun 02 2019 - 09:00:44 PDT)
[AMBER] temperature not reaching target value in heating simulation
(Sun Jun 02 2019 - 02:07:29 PDT)
Violeta Burns Casamayor
[AMBER] changes in periodic box dimensions after pmemd.cuda run
(Fri Jun 28 2019 - 17:26:42 PDT)
Wesley Michael Botello-Smith
Re: [AMBER] counting water molecules through transmembrane pore
(Wed Jun 12 2019 - 13:14:38 PDT)
Xia, Zhonghua
Re: [AMBER] MM-PBSA
(Tue Jun 18 2019 - 11:42:16 PDT)
Re: [AMBER] MM-PBSA
(Tue Jun 18 2019 - 11:19:43 PDT)
xmgign.126.com
[AMBER] The membran-water system ran out of the box
(Mon Jun 17 2019 - 23:41:40 PDT)
[AMBER] Some errors for the membrane system
(Sun Jun 02 2019 - 20:32:00 PDT)
Yeyue Xiong
[AMBER] Recommended CUDA version for Amber18-19 on RTX GPUs?
(Fri Jun 21 2019 - 13:01:53 PDT)
Yuan Hu
Re: [AMBER] Write out box dimensions in the trajectory
(Wed Jun 05 2019 - 08:16:13 PDT)
[AMBER] Write out box dimensions in the trajectory
(Tue Jun 04 2019 - 10:43:35 PDT)
Yuvraj Singh
[AMBER] Constant pH simulation of PyroPhosphate in Explicit solvent
(Mon Jun 17 2019 - 08:58:45 PDT)
Yuwei Song
[AMBER] [Amber]-help-messy rst output using Sander
(Wed Jun 12 2019 - 11:13:26 PDT)
Zachary Fallon
Re: [AMBER] parameter file for dUTP
(Tue Jun 04 2019 - 15:34:36 PDT)
Zhiyi Wu
[AMBER] File missing in the apr tutorial
(Tue Jun 04 2019 - 03:53:51 PDT)
zmatovic.kg.ac.rs
Re: [AMBER] stopping antechamber
(Fri Jun 28 2019 - 12:41:51 PDT)
Re: [AMBER] sqm.pdb structure
(Sat Jun 22 2019 - 17:26:02 PDT)
Re: [AMBER] sqm.pdb structure
(Sat Jun 22 2019 - 08:18:42 PDT)
谭畅
[AMBER] hbond
(Tue Jun 18 2019 - 23:25:51 PDT)
Last message date
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Sun Jun 30 2019 - 12:30:02 PDT
Archived on
: Wed Apr 24 2024 - 05:55:48 PDT
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