Amber Archive Feb 2015 by thread
- [AMBER] Problem with Ambertools14 Fugui (Sat Jan 31 2015 - 10:27:12 PST)
- [AMBER] Constructing a single Zwitterion in xleap Robert Molt (Sat Jan 31 2015 - 21:36:16 PST)
- [AMBER] missing atom of heme Fatemeh Sadat Alavi (Sun Feb 01 2015 - 00:14:31 PST)
- [AMBER] Create one larger averaged trajectory file ! Hadeer ELHabashy (Sun Feb 01 2015 - 02:36:25 PST)
- [AMBER] AMD stuck with v-limit exceeded error Hadeer ELHabashy (Sun Feb 01 2015 - 02:56:00 PST)
- [AMBER] reparametrize water molecule near metal site Jorgen Simonsen (Sun Feb 01 2015 - 11:21:58 PST)
- Re: [AMBER] Forcefield for DNA Nihal Korkmaz (Sun Feb 01 2015 - 11:25:18 PST)
- [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program vijay kumar narsapuram (Sun Feb 01 2015 - 12:59:16 PST)
- [AMBER] can not be a parameter fitting Takuya Uto (Sun Feb 01 2015 - 21:54:36 PST)
- [AMBER] (无主题) chemjxn.126.com (Sun Feb 01 2015 - 22:58:20 PST)
- [AMBER] parameterization chemjxn.126.com (Sun Feb 01 2015 - 23:22:40 PST)
- [AMBER] Issue during mmgbsa decomposition James Starlight (Mon Feb 02 2015 - 04:26:49 PST)
- [AMBER] error in equil.rst steps of AMBER Shreeramesh (Mon Feb 02 2015 - 06:32:51 PST)
- [AMBER] AmberTools14 installation Dhiraj Srivastava (Mon Feb 02 2015 - 11:25:25 PST)
- [AMBER] ante-MMPBSA IndexError: list index out of range Kenneth Huang (Mon Feb 02 2015 - 11:57:15 PST)
- [AMBER] Create a 2M urea box Ibrahim Said (Mon Feb 02 2015 - 12:33:06 PST)
- [AMBER] pmemd.cuda.MPI interruption error! 汪盛 (Mon Feb 02 2015 - 16:13:45 PST)
- Re: [AMBER] harmonic restraint file abdennour braka (Tue Feb 03 2015 - 02:47:58 PST)
- [AMBER] Analysis of the MMGBSA decomposition output James Starlight (Tue Feb 03 2015 - 06:34:44 PST)
- [AMBER] REGARDING GAUSSIAN BASED SIDE CHAIN MODEL OPTIMIZATION Swithin Hanosh (Tue Feb 03 2015 - 07:06:12 PST)
- [AMBER] Calculation of the number of internal waters during md simulation James Starlight (Tue Feb 03 2015 - 07:54:03 PST)
- [AMBER] LAST CALL: Free Energy Workshop, Münster, March 9-11, 2015 Vlad Cojocaru (Tue Feb 03 2015 - 12:35:33 PST)
- [AMBER] Second announcement: AMBER Workshop - Haifa Israel, Sun Apr 26th to 30th. Ross Walker (Tue Feb 03 2015 - 13:44:39 PST)
- [AMBER] have not atom type Fatemeh Sadat Alavi (Tue Feb 03 2015 - 22:20:36 PST)
- [AMBER] confusion in md run Robin Jain (Wed Feb 04 2015 - 00:12:43 PST)
- [AMBER] REGARDING GAUSSIAN BASED SIDE CHAIN MODEL OPTIMIZATION Swithin Hanosh (Wed Feb 04 2015 - 01:30:08 PST)
- [AMBER] no parameter for nicotine Harmeet Kaur (Wed Feb 04 2015 - 02:07:40 PST)
- [AMBER] Error while running antechamber and tleap for silver salt of carboxylic acid Shreeramesh (Wed Feb 04 2015 - 03:06:06 PST)
- [AMBER] seek help 新生大侠 (Wed Feb 04 2015 - 03:42:57 PST)
- Re: [AMBER] bad atom type: OA Houcemeddine Othman (Wed Feb 04 2015 - 04:26:09 PST)
- [AMBER] Amber14 hardware setup Sofia Vasilakaki (Wed Feb 04 2015 - 04:59:49 PST)
- [AMBER] MD cis-azobenzene error Anya Leach (Wed Feb 04 2015 - 13:38:43 PST)
- [AMBER] Xeon Phi Novosielski, Ryan (Wed Feb 04 2015 - 15:48:21 PST)
- [AMBER] ERRORS AND FATAL ERRORS (Apparently died to faulty connections) Evans, Shalton (Wed Feb 04 2015 - 22:22:39 PST)
- [AMBER] Error while running tleap for carboxylate anion Shreeramesh (Thu Feb 05 2015 - 01:18:37 PST)
- [AMBER] Real time event with amber mds with shake Hadeer ELHabashy (Thu Feb 05 2015 - 03:49:28 PST)
- Re: [AMBER] bash scripting for MD tasks James Starlight (Thu Feb 05 2015 - 06:10:34 PST)
- [AMBER] ACS COMP Division awards for Fall 2015 National Meeting in Boston Carlos Simmerling (Thu Feb 05 2015 - 08:55:09 PST)
- Re: [AMBER] FATAL: Atom .R<RU5 13>.A<P 29> does not have a type. Mahad Gatti Iou (Thu Feb 05 2015 - 08:58:31 PST)
- [AMBER] xleap syntax error Ahmet yıldırım (Thu Feb 05 2015 - 09:26:53 PST)
- [AMBER] CUDA 5.0 vs 6.5 Ryan Novosielski (Thu Feb 05 2015 - 12:48:03 PST)
- [AMBER] charmmlipid2amber.x Chris Chris (Thu Feb 05 2015 - 19:28:15 PST)
- [AMBER] Restraint bugs after most recent patch Niel Henriksen (Thu Feb 05 2015 - 22:41:26 PST)
- [AMBER] MCPB chemjxn.126.com (Fri Feb 06 2015 - 00:21:14 PST)
- Re: [AMBER] Error while running MD for carboxylate anion Shreeramesh (Fri Feb 06 2015 - 01:25:44 PST)
- [AMBER] MD JOB was terminated before achieving the No. of steps Shreeramesh (Fri Feb 06 2015 - 01:28:53 PST)
- [AMBER] Query regarding Dynamics Studies Ruchika Bhat (Fri Feb 06 2015 - 05:03:26 PST)
- [AMBER] Assignment of charges for Guanidine Ibrahim Said (Fri Feb 06 2015 - 07:54:14 PST)
- [AMBER] cis peptide bond Dhiraj Srivastava (Fri Feb 06 2015 - 08:40:34 PST)
- [AMBER] protein falls apart on explicit solvation md Anupam Goel (Fri Feb 06 2015 - 12:04:36 PST)
- [AMBER] vmd_box_dims.sh Chris Chris (Fri Feb 06 2015 - 20:18:22 PST)
- [AMBER] Strange md and RMSD behavior Hadeer ELHabashy (Sat Feb 07 2015 - 13:22:43 PST)
- [AMBER] New web server for setup of membrane simulation systems Jochen Hub (Sun Feb 08 2015 - 03:32:28 PST)
- [AMBER] Output Forces Acting of Each Atom During MD Simulation using Amber14 Emmanuel (Sun Feb 08 2015 - 16:05:23 PST)
- [AMBER] Inexperienced User Trying to Solve Simulation Blowup Robert Molt (Sun Feb 08 2015 - 20:02:03 PST)
- [AMBER] Test Andreas Goetz (Mon Feb 09 2015 - 07:41:57 PST)
- [AMBER] unexpected behaviour with antechamber Hannes Loeffler (Mon Feb 09 2015 - 08:31:07 PST)
- [AMBER] Average Internal Coordinates in cpptraj Dr. Robert Molt Jr. (Mon Feb 09 2015 - 08:37:52 PST)
- [AMBER] How to find out buried waters? Jose Borreguero (Mon Feb 09 2015 - 12:40:35 PST)
- [AMBER] memory issue in mmpbsa_py_nabnmode Marek Maly (Mon Feb 09 2015 - 15:54:20 PST)
- [AMBER] On the crushing of the membrane protein simulation James Starlight (Tue Feb 10 2015 - 07:44:01 PST)
- [AMBER] antechamber error Harmeet Kaur (Tue Feb 10 2015 - 23:07:13 PST)
- [AMBER] Fwd: MMPBSA a.mohseni (Wed Feb 11 2015 - 00:59:55 PST)
- [AMBER] calculating HB lifetime Vijay Achari (Wed Feb 11 2015 - 02:18:08 PST)
- [AMBER] Density equilibration crash in cuda Kshatresh Dutta Dubey (Wed Feb 11 2015 - 03:36:33 PST)
- [AMBER] Number of molecules for md calculations Ibrahim Said (Wed Feb 11 2015 - 08:57:30 PST)
- [AMBER] list of atomic coordinates involved in solvent accessible area Iqbal, Muhammad Sajid (Wed Feb 11 2015 - 14:26:51 PST)
- [AMBER] alkynes in GAFF Rebeca García Fandiño (Thu Feb 12 2015 - 01:42:06 PST)
- [AMBER] aMD and scaled MD in amber 14 Neha Gandhi (Thu Feb 12 2015 - 04:59:24 PST)
- [AMBER] MMPBSA - standard deviation (again) George Tzotzos (Thu Feb 12 2015 - 06:29:04 PST)
- [AMBER] Announcement: Release of DOCK 6.7 Scott Brozell (Thu Feb 12 2015 - 16:27:51 PST)
- [AMBER] Water diffusion - in 2D and 3D Vijay Achari (Thu Feb 12 2015 - 22:11:24 PST)
- [AMBER] hbond analysis Ayesha Fatima (Thu Feb 12 2015 - 23:48:42 PST)
- [AMBER] rotational diffusion Vijay Achari (Fri Feb 13 2015 - 03:00:08 PST)
- [AMBER] assignment of Water molecules Ibrahim Said (Fri Feb 13 2015 - 04:13:47 PST)
- [AMBER] Umbrella Sampling Mahmood Jasim (Fri Feb 13 2015 - 04:36:08 PST)
- [AMBER] d 김준기 (Fri Feb 13 2015 - 07:26:27 PST)
- [AMBER] Error: Restart File Corrupted Edward Kalkreuter (Fri Feb 13 2015 - 10:03:10 PST)
- [AMBER] angles values in GAFF for alkynes Rebeca García Fandiño (Fri Feb 13 2015 - 10:19:12 PST)
- [AMBER] csv file for DPC Sylvester Tumusiime (Fri Feb 13 2015 - 12:41:39 PST)
- [AMBER] pmemd.cuda error cudaMemcpy GpuBuffer:: BERGY (Fri Feb 13 2015 - 22:38:35 PST)
- [AMBER] pbsa zahra khatti (Sat Feb 14 2015 - 21:31:46 PST)
- [AMBER] Question about hbond analysis 徐晓庶 (Sat Feb 14 2015 - 23:06:51 PST)
- [AMBER] pressure fluctuation problem Aditya Sarkar (Sun Feb 15 2015 - 00:05:10 PST)
- [AMBER] pbsa zahra khatti (Sun Feb 15 2015 - 10:53:34 PST)
- [AMBER] amber14 hangs on Python datetime module Robert Wohlhueter (Sun Feb 15 2015 - 11:06:55 PST)
- [AMBER] Could not find vdW (or other) parameters for type: Fe2+ Pragya Priyadarshini (Sun Feb 15 2015 - 19:45:46 PST)
- [AMBER] dont have atom type Fatemeh Sadat Alavi (Mon Feb 16 2015 - 04:44:10 PST)
- [AMBER] AMBER: MPI run issue Bajarang Kumbhar (Mon Feb 16 2015 - 05:38:31 PST)
- [AMBER] combining trajectories Ayesha Fatima (Mon Feb 16 2015 - 06:29:05 PST)
- [AMBER] torsion restrain Lara rajam (Mon Feb 16 2015 - 07:16:20 PST)
- [AMBER] reweighing aMD trajectory Asmita Gupta (Mon Feb 16 2015 - 07:46:43 PST)
- [AMBER] MMGBSA question George Tzotzos (Mon Feb 16 2015 - 11:11:28 PST)
- [AMBER] MMGBSA question George Tzotzos (Mon Feb 16 2015 - 11:53:26 PST)
- [AMBER] Announcement: "Hands-On" Workshop on Computational Biophysics in Urbana, IL (April 6-10, 2015) Jodi Ann Hadden (Mon Feb 16 2015 - 13:41:55 PST)
- [AMBER] solute-solvent hbond fraction value is more than 1.0 Vijay Achari (Mon Feb 16 2015 - 23:14:55 PST)
- [AMBER] Regarding AmberTool 14 installation MOHD HOMAIDUR RAHMAN (Tue Feb 17 2015 - 00:08:40 PST)
- [AMBER] [MGMS-DS]: Molecular Modelling Workshop March 9-11, 2015 in Erlangen, Germany Harald Lanig (Tue Feb 17 2015 - 06:10:03 PST)
- [AMBER] Question regarding the calculation of binding constants Kornelius Zeth (Tue Feb 17 2015 - 07:17:06 PST)
- [AMBER] Can cpptraj-hbond report the lifetimes of H-bonds between protein and water? Jose Borreguero (Tue Feb 17 2015 - 07:57:46 PST)
- [AMBER] Invitation to Attend Computational Chemical Biology Conference (Aug 6th to 9th 2015), Cairns, Australia (http://tinyurl.com/nyblv7o) Ross Walker (Tue Feb 17 2015 - 08:26:26 PST)
- [AMBER] MMPBSA pairwise decomposition error George Tzotzos (Tue Feb 17 2015 - 12:00:34 PST)
- [AMBER] Simulations in CCl4 pradeep pant (Tue Feb 17 2015 - 23:14:38 PST)
- [AMBER] Distance/Angle distribution along the trajectory using cpptraj James Starlight (Wed Feb 18 2015 - 01:51:28 PST)
- [AMBER] restraining the torsion Lara rajam (Wed Feb 18 2015 - 07:03:09 PST)
- [AMBER] cpptraj hbond analysis Ayesha Fatima (Wed Feb 18 2015 - 07:42:28 PST)
- [AMBER] Forces from Potential Ahmed Ayoub (Wed Feb 18 2015 - 08:39:13 PST)
- [AMBER] Help creating custom monosaccharide unit in Glycam Gustavo Seabra (Wed Feb 18 2015 - 10:54:40 PST)
- [AMBER] Bad atom type error in MMPBSA Kenneth Huang (Wed Feb 18 2015 - 13:02:48 PST)
- [AMBER] problem with RMSD for small molecule Maryam Hamzehee (Thu Feb 19 2015 - 01:45:06 PST)
- [AMBER] cpptraj hbond analysis Ayesha Fatima (Thu Feb 19 2015 - 01:59:46 PST)
- [AMBER] rmsavgcorr Jacopo Sgrignani (Thu Feb 19 2015 - 07:46:17 PST)
- [AMBER] Help calculating RMSD between two proteins Nicole Ippolito (Thu Feb 19 2015 - 10:09:29 PST)
- [AMBER] ired t1 relaxation time Khanna, Tarun (Thu Feb 19 2015 - 10:56:57 PST)
- [AMBER] ANTECHAMBER: error in mol2 file Valentina Romano (Fri Feb 20 2015 - 01:59:45 PST)
- [AMBER] Error while running tleap for the ligand containing two chlorine atoms Shreeramesh (Fri Feb 20 2015 - 02:58:03 PST)
- [AMBER] Lipid14 POPE lipids Joseph Baker (Fri Feb 20 2015 - 04:42:09 PST)
- [AMBER] Sander in background Valentina Romano (Fri Feb 20 2015 - 05:36:28 PST)
- [AMBER] hbond analysis Ayesha Fatima (Fri Feb 20 2015 - 05:37:40 PST)
- [AMBER] LIPID14 and ff15SB Ghulam Mustafa (Fri Feb 20 2015 - 09:06:35 PST)
- [AMBER] Solvent Box Wrapping Issue Zhang, Sixue (Fri Feb 20 2015 - 13:04:43 PST)
- [AMBER] vlimit exceeded for step Fatemeh Sadat Alavi (Sat Feb 21 2015 - 03:51:15 PST)
- [AMBER] Error: Expected DCD block size of 48, got -1029941464 Thomas Evangelidis (Sat Feb 21 2015 - 13:06:03 PST)
- [AMBER] rms: Warning: [rms] Not all arguments handled: [ rmsd.agr ] George Tzotzos (Sat Feb 21 2015 - 13:14:45 PST)
- [AMBER] cpptraj hbond lifetime problem Ayesha Fatima (Sun Feb 22 2015 - 01:59:56 PST)
- [AMBER] A tool to analyze amberesults Valentina Romano (Sun Feb 22 2015 - 06:56:15 PST)
- [AMBER] Problem in generating CCL4 solvent Box pradeep pant (Sun Feb 22 2015 - 10:02:44 PST)
- [AMBER] Fwd: Amber tleap error Garisekurthi Satheesh (Sun Feb 22 2015 - 19:30:09 PST)
- [AMBER] RV: segmentation fault when running parmchk belen nieto (Mon Feb 23 2015 - 02:45:43 PST)
- [AMBER] Help in choosing right MD tool anu chandra (Mon Feb 23 2015 - 04:09:04 PST)
- [AMBER] atomicfluct issue George Tzotzos (Mon Feb 23 2015 - 05:30:04 PST)
- [AMBER] Regarding ff02 force field and RESP method documentation Martin Olsson (Mon Feb 23 2015 - 07:50:13 PST)
- [AMBER] how to find out if a prmtop file was created with ff12 or ff14 Thomas Evangelidis (Mon Feb 23 2015 - 08:27:37 PST)
- [AMBER] cpptraj: H-bond clarification sought George Tzotzos (Mon Feb 23 2015 - 10:12:33 PST)
- [AMBER] Create a unit of mixture Ibrahim Said (Mon Feb 23 2015 - 10:56:59 PST)
- [AMBER] Steered MD using the jar=1 option Joseph Baker (Mon Feb 23 2015 - 14:07:08 PST)
- [AMBER] Invitation for proposing a book chapter Maryam Hamzehee (Mon Feb 23 2015 - 23:20:20 PST)
- [AMBER] On the collective dynamics in terms of NMA and PCA James Starlight (Tue Feb 24 2015 - 02:23:55 PST)
- [AMBER] Announcement: release of FESetup 1.1 Hannes Loeffler (Tue Feb 24 2015 - 07:48:25 PST)
- [AMBER] Can I use the presence of a particular hydrogen bond as a condition to filter out frames? Jose Borreguero (Tue Feb 24 2015 - 10:16:18 PST)
- [AMBER] REGARDING WARNINGS RETURNED DURING FORCE FIELD GENERATION Swithin Hanosh (Tue Feb 24 2015 - 11:19:27 PST)
- [AMBER] Bond Energy Term for a TIP3P Water Zhang, Sixue (Tue Feb 24 2015 - 11:30:55 PST)
- [AMBER] Closest residues to an atom in ptraj Alessandra Lacetera (Tue Feb 24 2015 - 11:42:06 PST)
- [AMBER] Unexpected behavior of trajout after invoking filter: Bug? Jose Borreguero (Tue Feb 24 2015 - 14:57:59 PST)
- [AMBER] Chamber problem Shukla, Saurabh (Tue Feb 24 2015 - 17:24:05 PST)
- [AMBER] H-REMD failure on GPU Carlo Guardiani (Wed Feb 25 2015 - 08:57:43 PST)
- [AMBER] An Amber Lipid Force Field Tutorial: problem with shell script Chris Gaughan (Wed Feb 25 2015 - 20:02:58 PST)
- [AMBER] Center of mass restraints work on pmemd.MPI, but not on the GPU mmaestre (Wed Feb 25 2015 - 20:19:51 PST)
- [AMBER] Cofactor parametrization Francesca Tessaro (Thu Feb 26 2015 - 06:45:59 PST)
- [AMBER] MMGBSA: calculation of deltaG of ligand binding at dimer interface George Tzotzos (Thu Feb 26 2015 - 07:46:45 PST)
- [AMBER] Can't get shell script to work with Lipid tutorial Chris Chris (Thu Feb 26 2015 - 09:52:14 PST)
- [AMBER] CUDA- Error pmemd Lipid Membrane Romero, Raquel (Thu Feb 26 2015 - 18:02:11 PST)
- [AMBER] FATAL: Atom .R<GRA 1>.A<H31 197> does not have a type. Evans, Shalton (Thu Feb 26 2015 - 22:51:43 PST)
- [AMBER] Parallel GPU calculation Stefano Motta (Fri Feb 27 2015 - 03:46:42 PST)
- [AMBER] GTX980 PERFORMANCE carmendigiovanni75.alice.it (Fri Feb 27 2015 - 05:31:01 PST)
- [AMBER] SDPC and SAPC lipid bilayer Hector A. Baldoni (Fri Feb 27 2015 - 06:21:14 PST)
- Re: [AMBER] REMD jobs crashing repeatedly on GPUs Scott Brozell (Fri Feb 27 2015 - 09:33:03 PST)
- [AMBER] Inability to use antechamber on Anion Robert Molt (Fri Feb 27 2015 - 18:04:32 PST)
- [AMBER] problem with running tutorial C1 Maryam Hamzehee (Fri Feb 27 2015 - 23:14:21 PST)
- [AMBER] help in sdf Robin Jain (Sat Feb 28 2015 - 08:39:58 PST)
- Last message date: Sat Feb 28 2015 - 13:30:02 PST
- Archived on: Wed Oct 30 2024 - 05:55:07 PDT
