Amber Archive Apr 2015 by thread
- Re: [AMBER] Multiple MEPs option in R.E.D tools Yip Yew Mun (Tue Mar 31 2015 - 20:08:17 PDT)
- Re: [AMBER] AMBER14 pmemd.cuda.MPI : *** in mdout files Himanshu Joshi (Tue Mar 31 2015 - 20:32:38 PDT)
- [AMBER] 发送给你的文件 chemjxn (Tue Mar 31 2015 - 23:29:00 PDT)
- [AMBER] MCPB subprogram problem chemjxn (Tue Mar 31 2015 - 23:41:50 PDT)
- [AMBER] New Force Field Jason Swails (Wed Apr 01 2015 - 04:12:07 PDT)
- Re: [AMBER] Help regarding appropriate analysis for correlated motion using cpptraj Jason Swails (Wed Apr 01 2015 - 06:04:26 PDT)
- Re: [AMBER] MMPBSA error Abhishek TYAGI (Wed Apr 01 2015 - 06:35:10 PDT)
- [AMBER] error **** in output file with wrapping first molecule on GPU Quynh Vo (Wed Apr 01 2015 - 23:00:08 PDT)
- [AMBER] Error while running MMPBSA Shreeramesh (Thu Apr 02 2015 - 00:00:59 PDT)
- Re: [AMBER] EGB and ESCF might not be converged if the net charge not equal to 0 in the QM/MM-GBSA psu4.uic.edu (Thu Apr 02 2015 - 00:27:31 PDT)
- Re: [AMBER] Restrained MD James Starlight (Thu Apr 02 2015 - 05:38:02 PDT)
- [AMBER] Build long polymer from the monomer using Xleap James Starlight (Thu Apr 02 2015 - 05:41:24 PDT)
- [AMBER] mmbsa.py issue with the complex.parmtop James Starlight (Thu Apr 02 2015 - 06:17:05 PDT)
- [AMBER] Sander QMMM Bomb Problem Gulsevin,Alican (Thu Apr 02 2015 - 08:52:30 PDT)
- [AMBER] FW: amber14 errors IBRAHIM M ABDELRADY (Thu Apr 02 2015 - 11:16:28 PDT)
- Re: [AMBER] How to obtain potential energy using mdcrd trajectories in AMBER12 Brian Radak (Thu Apr 02 2015 - 12:06:23 PDT)
- [AMBER] Lipid Conversion from Charmm PDB to Lipid14 PDB Wong, Sook (NIH/NCATS) [V] (Thu Apr 02 2015 - 12:35:27 PDT)
- [AMBER] MMPBSA issues with ff12SB Neha Gandhi (Fri Apr 03 2015 - 08:34:21 PDT)
- [AMBER] Trouble recomputing aMD boost from amdlog/mdout Brian Radak (Fri Apr 03 2015 - 12:42:02 PDT)
- [AMBER] MMPBSA.py.MPI Installation Failure Laura Tociu (Sat Apr 04 2015 - 11:34:04 PDT)
- [AMBER] Question Regarding reduce function of Antechamber Ziheng Wang (Sat Apr 04 2015 - 12:34:22 PDT)
- [AMBER] The Meaning of Some Parameters wjli (Sun Apr 05 2015 - 05:14:27 PDT)
- [AMBER] barosts command in amber 12 Chris Gaughan (Sun Apr 05 2015 - 11:04:52 PDT)
- [AMBER] query sanjaykumar.imtech.res.in (Mon Apr 06 2015 - 01:46:29 PDT)
- [AMBER] Radial distribution function (RDF) for sugars in disaccharides Vijay Achari (Mon Apr 06 2015 - 19:51:19 PDT)
- [AMBER] REGARDING ATOM TYPE ERROR Swithin Hanosh (Mon Apr 06 2015 - 22:17:24 PDT)
- [AMBER] The force field used in MCPB wjli (Mon Apr 06 2015 - 23:28:41 PDT)
- [AMBER] typo error in the amber14 manual Vijay Achari (Tue Apr 07 2015 - 00:41:04 PDT)
- [AMBER] The Stand Model in MCPB wjli (Tue Apr 07 2015 - 02:00:29 PDT)
- [AMBER] error generating P450 prmtop incrd file Vaibhav Dixit (Tue Apr 07 2015 - 04:54:14 PDT)
- [AMBER] potential issue with energy drift Steven Ramsey (Tue Apr 07 2015 - 06:30:25 PDT)
- [AMBER] Calculating protein center of mass (COM) using vector command George Green (Tue Apr 07 2015 - 07:51:11 PDT)
- [AMBER] FW: TLEAP Fatal Error Wong, Sook (NIH/NCATS) [V] (Tue Apr 07 2015 - 08:15:15 PDT)
- [AMBER] COM distance restraints and pmemd.cuda Ilyas Yildirim (Tue Apr 07 2015 - 10:12:51 PDT)
- [AMBER] Possible bug in nativecontacts command of cpptraj (v14)? Samuel Bowerman (Tue Apr 07 2015 - 10:52:57 PDT)
- [AMBER] Boltzman Weights from MD trajectory Emilio Angelina (Tue Apr 07 2015 - 11:33:33 PDT)
- [AMBER] Energy drift issue Steven Ramsey (Tue Apr 07 2015 - 12:52:55 PDT)
- [AMBER] Error message in Amber14 tutorial A16 Michael Shokhen (Tue Apr 07 2015 - 12:57:12 PDT)
- [AMBER] Error in tutorial A16, Amber 14 Michael Shokhen (Tue Apr 07 2015 - 23:16:48 PDT)
- [AMBER] AHTECHAMBER - G09 Sanja Zivanovic (Wed Apr 08 2015 - 06:33:10 PDT)
- [AMBER] defining residues in steered molecular dynamics Ayesha Fatima (Wed Apr 08 2015 - 07:57:53 PDT)
- [AMBER] Visualization of the MMGBSA per-residue decomposition James Starlight (Wed Apr 08 2015 - 09:43:02 PDT)
- [AMBER] xleap Menu bar problems Pierre Bertin (Wed Apr 08 2015 - 18:21:20 PDT)
- [AMBER] MMBP(GB)SA free energy decomposition error: sander failed with prmtop maryam azimzadehirani (Wed Apr 08 2015 - 20:40:05 PDT)
- [AMBER] larger bonds between protein atoms Vaibhav Dixit (Thu Apr 09 2015 - 04:15:09 PDT)
- [AMBER] Problem with MMPBSA.py.MPI for nmode Sofia Vasilakaki (Thu Apr 09 2015 - 07:39:15 PDT)
- [AMBER] a question for hydrocarbons simulation using amber FF Nahid Khiabani (Thu Apr 09 2015 - 13:33:43 PDT)
- [AMBER] Organic solvent from imported molecule (e.g. : nitric acid) Pierre Bertin (Thu Apr 09 2015 - 18:51:52 PDT)
- [AMBER] How to use the mmpbsa.py to calcualte the free energy of a modified protein ? windy (Thu Apr 09 2015 - 19:29:59 PDT)
- [AMBER] Diffusion constant calculation pooja chahal (Thu Apr 09 2015 - 23:20:24 PDT)
- [AMBER] Force Field Parameters for Monoamino Acids at acidic and basic conditions? Alain Chaumont (Fri Apr 10 2015 - 00:08:21 PDT)
- [AMBER] MMPBSA on NAMD DCD Trajectories Ahmed Ezat (Fri Apr 10 2015 - 03:55:25 PDT)
- [AMBER] cpptraj write data from runanalysis Gard Nelson (Fri Apr 10 2015 - 11:29:45 PDT)
- [AMBER] Unsupported CUDA version 7.0 detected. Emilio Angelina (Fri Apr 10 2015 - 13:38:09 PDT)
- [AMBER] Invitation to Computational Chemical Biology Conference (Aug 6th to 9th 2015), Cairns, Australia (http://tinyurl.com/nyblv7o) Ross Walker (Fri Apr 10 2015 - 15:25:23 PDT)
- [AMBER] Does atomicflut byres report the fluctuations of the residue CM? Jose Borreguero (Fri Apr 10 2015 - 15:44:38 PDT)
- [AMBER] intercalations Arjun Sharma (Fri Apr 10 2015 - 16:36:30 PDT)
- [AMBER] Bad atom Type in MMPBSA.py wjli (Fri Apr 10 2015 - 19:35:15 PDT)
- [AMBER] Quasi-harmonic Entropy Calculated using MMPBSA.py Laura Tociu (Fri Apr 10 2015 - 19:56:48 PDT)
- [AMBER] a question for hydrocarbons simulation using amber FF Nahid Khiabani (Sat Apr 11 2015 - 00:09:14 PDT)
- [AMBER] error in minimization Carlos Romero (Sat Apr 11 2015 - 13:55:32 PDT)
- [AMBER] Error Adnan Gulzar (Sat Apr 11 2015 - 15:18:53 PDT)
- [AMBER] Amino acid as ligand Dhiraj Srivastava (Sat Apr 11 2015 - 20:06:20 PDT)
- [AMBER] a question for hydrocarbons simulation using amber FF Nahid Khiabani (Sun Apr 12 2015 - 03:33:15 PDT)
- [AMBER] Arrangement of molecules in 3D packed state jacob wick (Sun Apr 12 2015 - 11:30:25 PDT)
- [AMBER] Mmgbsa decomposition James Starlight (Mon Apr 13 2015 - 01:19:01 PDT)
- [AMBER] AMBER parametrization questions Jeffrey Teillet (Mon Apr 13 2015 - 06:20:11 PDT)
- [AMBER] Charmm force field parameters in Amber anu chandra (Mon Apr 13 2015 - 06:33:30 PDT)
- [AMBER] is it possible to output the trajectory of the center of mass of the residues? Jose Borreguero (Mon Apr 13 2015 - 07:05:51 PDT)
- [AMBER] hydrogen bond analysis using cpptraj in amber tools 14 Atila Petrosian (Tue Apr 14 2015 - 01:25:27 PDT)
- [AMBER] Restart file with velocity loic etheve (Tue Apr 14 2015 - 03:40:34 PDT)
- [AMBER] REGARDING ENERGY MINIMISATION Swithin Hanosh (Tue Apr 14 2015 - 04:42:26 PDT)
- [AMBER] Community network analysis for the Amber trajectories James Starlight (Tue Apr 14 2015 - 07:25:27 PDT)
- [AMBER] Calculating Cp values from NPT simulations using ptraj Vivek Shankar Bharadwaj (Tue Apr 14 2015 - 14:42:13 PDT)
- [AMBER] Deletion of H atoms from pdb file used for MD simulations muhammad tahir ayub (Tue Apr 14 2015 - 23:35:51 PDT)
- [AMBER] REGARDING ENERGY MINIMISATION Swithin Hanosh (Wed Apr 15 2015 - 05:32:32 PDT)
- [AMBER] The influence of parameters in md.in when restart a MD (from rst file) windy (Wed Apr 15 2015 - 07:05:31 PDT)
- [AMBER] Error with quasi-harmonic MMPBSA.py calculations Abhishek TYAGI (Wed Apr 15 2015 - 21:26:20 PDT)
- Re: [AMBER] Evaluating hydrogen boding lifetime Vijay Achari (Wed Apr 15 2015 - 23:41:54 PDT)
- [AMBER] Alanin scanning MMGBSA.py error: TypeError: not all arguments converted during string formatting maryam azimzadehirani (Thu Apr 16 2015 - 00:06:05 PDT)
- [AMBER] Writing out restart files gepaula.web.de (Thu Apr 16 2015 - 07:14:21 PDT)
- [AMBER] all in one pc for MD simulation calculations Atila Petrosian (Thu Apr 16 2015 - 07:50:45 PDT)
- [AMBER] NMode Analysis Using Truncated Trajectory Laura Tociu (Thu Apr 16 2015 - 11:53:19 PDT)
- Re: [AMBER] deletion of H atoms for pdb file hannes.loeffler.stfc.ac.uk (Thu Apr 16 2015 - 12:16:34 PDT)
- [AMBER] Could anyone tell me how to run targeted MD correctly 肖立 (Thu Apr 16 2015 - 23:45:08 PDT)
- [AMBER] Carbon nanotube simulation Pierre Bertin (Thu Apr 16 2015 - 23:51:08 PDT)
- [AMBER] ligand-solvent interaction energy Hannes Loeffler (Fri Apr 17 2015 - 02:23:41 PDT)
- [AMBER] Batch leap error! Pallavi Mohanty (Fri Apr 17 2015 - 04:02:00 PDT)
- [AMBER] How to resolve the problem when amber14 configured with cuda 6.5 金毅 (Fri Apr 17 2015 - 23:28:41 PDT)
- [AMBER] Problem regarding PMF curve Shubhadip Das (Sun Apr 19 2015 - 08:49:15 PDT)
- [AMBER] One chain of protein going out of box Shukla, Saurabh (Sun Apr 19 2015 - 18:27:55 PDT)
- [AMBER] Problem in running with steered MD 肖立 (Sun Apr 19 2015 - 18:29:42 PDT)
- [AMBER] In MMPBSY.py , how to set interval value when large conformation change ? windy (Mon Apr 20 2015 - 01:41:27 PDT)
- [AMBER] regarding .prmtop file generation neha chaudhary (Mon Apr 20 2015 - 03:58:06 PDT)
- [AMBER] PCA analysis Muthukumaran R (Mon Apr 20 2015 - 04:44:46 PDT)
- [AMBER] cpptraj writting box coordinates issue CHAMI F. (Mon Apr 20 2015 - 08:00:09 PDT)
- [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Vaibhav Dixit (Tue Apr 21 2015 - 02:29:07 PDT)
- [AMBER] ATTN needs revision Sanja Zivanovic (Tue Apr 21 2015 - 08:13:35 PDT)
- [AMBER] The error occurs when I set radiopt =1 in MMPBSA.py wliu (Tue Apr 21 2015 - 08:28:07 PDT)
- [AMBER] install Amber 11 and AmberTools 1.5 on CentoS 6.3 Atila Petrosian (Tue Apr 21 2015 - 12:02:46 PDT)
- [AMBER] Amber GPU Segmentation fault AJ Venkatakrishnan (Tue Apr 21 2015 - 15:29:31 PDT)
- [AMBER] install Amber 11 and AmberTools 1.5 on CentoS 6.3 Atila Petrosian (Tue Apr 21 2015 - 21:18:05 PDT)
- [AMBER] Any timeline for TI on GPU's? Ucisik, Melek Nihan (Wed Apr 22 2015 - 09:39:56 PDT)
- [AMBER] CENTOS 6.6 :ERROR - INSTALLATION OF AMBERTOOLS14/AMBER14 vitonoja.yahoo.com (Wed Apr 22 2015 - 20:06:11 PDT)
- [AMBER] mcpb problem chemjxn (Wed Apr 22 2015 - 21:12:08 PDT)
- [AMBER] AMBER 14 installation problem Sanjib Paul (Wed Apr 22 2015 - 22:49:14 PDT)
- Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program vijay kumar narsapuram (Thu Apr 23 2015 - 03:15:09 PDT)
- [AMBER] Free energy calculation of ligand binding energy: Thermodynamic integration - pmemd - single topology - vdw vladimir.palivec.marge.uochb.cas.cz (Thu Apr 23 2015 - 08:26:11 PDT)
- [AMBER] water box for steered md amber14 Asmita Gupta (Thu Apr 23 2015 - 10:50:54 PDT)
- [AMBER] DNA partial charges in Amber library jacob wick (Thu Apr 23 2015 - 22:23:08 PDT)
- [AMBER] Simulations at High temperature (425K) Biswa Ranjan Meher (Fri Apr 24 2015 - 07:17:17 PDT)
- [AMBER] mcpb problem chemjxn (Sat Apr 25 2015 - 01:17:20 PDT)
- [AMBER] Regarding running to independent simulations Soumendranath Bhakat (Sat Apr 25 2015 - 03:10:36 PDT)
- [AMBER] charmmlipid2amber2.py error Gözde YALÇIN (Sat Apr 25 2015 - 04:35:51 PDT)
- [AMBER] segmentation fault in AmberTool 14.25 MOHD HOMAIDUR RAHMAN (Sat Apr 25 2015 - 07:56:44 PDT)
- [AMBER] close contacts in equilibrated structure Asmita Gupta (Sat Apr 25 2015 - 08:37:25 PDT)
- [AMBER] the vectors of the moment of inertia protein CHAMI F. (Sat Apr 25 2015 - 09:07:07 PDT)
- [AMBER] problem with CHAMBER sudipta (Sat Apr 25 2015 - 11:21:19 PDT)
- [AMBER] charmmlipid2amber.py error Gözde YALÇIN (Sat Apr 25 2015 - 11:39:33 PDT)
- [AMBER] mpirun error shahab shariati (Sun Apr 26 2015 - 09:23:40 PDT)
- [AMBER] Quasi-harmonic Approximation Using a Trajectory Stripped of Hydrogens Laura Tociu (Sun Apr 26 2015 - 20:35:08 PDT)
- [AMBER] Segmentation fault in AmberTool 14.25 MOHD HOMAIDUR RAHMAN (Sun Apr 26 2015 - 23:20:15 PDT)
- [AMBER] parameterization Zn2+ with MCPB chemjxn (Mon Apr 27 2015 - 00:42:48 PDT)
- [AMBER] Questions about T-REMD lipengfei (Mon Apr 27 2015 - 05:30:45 PDT)
- [AMBER] cpptraj V14.25 issues with old Amber topology files (Amber 11) CHAMI F. (Mon Apr 27 2015 - 07:11:32 PDT)
- [AMBER] how to run non standard simulation muhammad tahir ayub (Mon Apr 27 2015 - 11:39:46 PDT)
- [AMBER] Antechamber Algorithm for Atom Type Robert Molt (Mon Apr 27 2015 - 18:19:57 PDT)
- [AMBER] Is there NHE cap in the ff02 library files? Yip Yew Mun (Mon Apr 27 2015 - 21:06:06 PDT)
- [AMBER] Fwd: Tleap atom type - template not found Balaji Selvam (Mon Apr 27 2015 - 23:02:29 PDT)
- [AMBER] Nmode analysis calculation problem for Implicit simulation. Bajarang Kumbhar (Tue Apr 28 2015 - 04:06:53 PDT)
- [AMBER] error in amber installation Atila Petrosian (Tue Apr 28 2015 - 04:14:55 PDT)
- [AMBER] pdbamb gives wrong resnumber Miguel Ángel Mompeán García (Tue Apr 28 2015 - 10:32:59 PDT)
- [AMBER] EGB and EEL Values in MM-GBSA -reg Muthukumaran R (Tue Apr 28 2015 - 11:03:58 PDT)
- [AMBER] dispersion for QM/MM missing parameters Jorgen Simonsen (Wed Apr 29 2015 - 00:17:16 PDT)
- [AMBER] The question about how to restart REMD simulation in AMBER12 and Langavin dynamics Wang Moye (Wed Apr 29 2015 - 00:46:23 PDT)
- [AMBER] Query about microsecond long simulation anu chandra (Wed Apr 29 2015 - 06:20:22 PDT)
- [AMBER] lipid simulation queries Bala subramanian (Wed Apr 29 2015 - 10:03:33 PDT)
- [AMBER] MMPBSA problem with calcium Francesco Gentile (Wed Apr 29 2015 - 11:15:36 PDT)
- [AMBER] restraining in xz coordinates only Samaneh Mesbahi (Wed Apr 29 2015 - 20:33:25 PDT)
- [AMBER] STRUCTURAL CHANGE AFTER HEATING Swithin Hanosh (Thu Apr 30 2015 - 05:06:44 PDT)
- [AMBER] restraining in xz coordinates only Samaneh Mesbahi (Thu Apr 30 2015 - 06:33:32 PDT)
- [AMBER] Bursary deadline, May 15, 2015: Drug Discovery Workshops Milan Thomas Exner (Thu Apr 30 2015 - 12:59:52 PDT)
- [AMBER] Bursary deadline, May 15, 2015: Drug Discovery Workshops Canada Thomas Exner (Thu Apr 30 2015 - 13:01:24 PDT)
- Last message date: Thu Apr 30 2015 - 16:00:02 PDT
- Archived on: Fri Dec 20 2024 - 05:55:12 PST
