Amber Archive Feb 2017 by thread
- Re: [AMBER] Fwd: Error during installation process Danu Fajar (Tue Jan 31 2017 - 09:37:49 PST)
- Re: [AMBER] Differences using leaprc.ff14SB from AmberTools15 and oldff/leaprc.ff14SB from AmberTools16 Daniel Roe (Tue Jan 31 2017 - 17:27:18 PST)
- Re: [AMBER] Multiple ligands in MMGBSA Elvis Martis (Tue Jan 31 2017 - 19:13:13 PST)
- Re: [AMBER] MMPBSA failed Albert (Tue Jan 31 2017 - 23:46:48 PST)
- Re: [AMBER] Regarding forcefields for Z-DNA Josh Berryman (Wed Feb 01 2017 - 01:38:24 PST)
- Re: [AMBER] clustering Sowmya Indrakumar (Wed Feb 01 2017 - 03:41:39 PST)
- [AMBER] APR - atom selection Andreas Tosstorff (Wed Feb 01 2017 - 05:05:56 PST)
- Re: [AMBER] Radical Carbon David Case (Wed Feb 01 2017 - 05:04:07 PST)
- [AMBER] [MMPBSA.py.MPI] Two questions (autoimage and parsing of output) Eiros Zamora, Juan (Wed Feb 01 2017 - 05:09:02 PST)
- Re: [AMBER] Give the correct charge to heme using antechamber Matteo Uggeri (Wed Feb 01 2017 - 06:36:41 PST)
- Re: [AMBER] constrain nitrate as bound and neutral Pengfei Li (Wed Feb 01 2017 - 07:48:35 PST)
- [AMBER] Thiophosphate paramters - AMBER Balaji Selvam (Wed Feb 01 2017 - 10:33:12 PST)
- [AMBER] Two Ph.D. positions in molecular simulations Jan Brezovsky (Wed Feb 01 2017 - 13:35:12 PST)
- [AMBER] cannot add bond Thakur, Abhishek (Wed Feb 01 2017 - 14:26:09 PST)
- [AMBER] Error in compiling pmemd.cuda Anton Perera (Wed Feb 01 2017 - 20:06:12 PST)
- [AMBER] Amber16 installation error SeungHyun Kim (Wed Feb 01 2017 - 22:39:28 PST)
- Re: [AMBER] Methods to count the different species Daniel Roe (Thu Feb 02 2017 - 06:59:17 PST)
- [AMBER] changing water molecules in water box Lara rajam (Thu Feb 02 2017 - 07:24:08 PST)
- [AMBER] Parameters for nucelotides Buteler,Maria del Pilar (Thu Feb 02 2017 - 08:15:12 PST)
- [AMBER] MTKpp.pdf manual Corum, Katharine W (Thu Feb 02 2017 - 09:08:19 PST)
- [AMBER] Tleap is making C instaed of Cl Thakur, Abhishek (Thu Feb 02 2017 - 09:09:45 PST)
- [AMBER] binding energy decomposition Jacopo Sgrignani (Thu Feb 02 2017 - 12:44:37 PST)
- Re: [AMBER] lj1264 pmemd.cuda Jason Swails (Thu Feb 02 2017 - 18:27:23 PST)
- [AMBER] protocol for simulating a system in NaCl using xleaP module zeba firdows (Thu Feb 02 2017 - 23:27:08 PST)
- [AMBER] Force Field for Ammonia? Gustavo Seabra (Fri Feb 03 2017 - 08:37:44 PST)
- [AMBER] parmed gromber issues inappropriate disulfide warning based on CYS/MET approach Chris Neale (Fri Feb 03 2017 - 13:57:39 PST)
- [AMBER] Number of threads in MMGBSA/MMPBSA calculations. Abhilash J (Fri Feb 03 2017 - 22:27:05 PST)
- [AMBER] ADDING WATER MOLECULES Subashini .K (Sat Feb 04 2017 - 02:54:49 PST)
- [AMBER] parmed add12_6_4 command error Marek Havrila (Sat Feb 04 2017 - 13:41:19 PST)
- Re: [AMBER] QM method used for force constants derivation in GAFF2 ? Marek Maly (Sat Feb 04 2017 - 19:24:56 PST)
- [AMBER] EPM2 Force field for CO2 Liyang Zhu (Sun Feb 05 2017 - 17:34:59 PST)
- [AMBER] Cannot open the main chain file after prepgen command Nikolay N. Kuzmich (Mon Feb 06 2017 - 04:09:52 PST)
- [AMBER] MMPBSA error konda003 . (Mon Feb 06 2017 - 09:08:42 PST)
- [AMBER] 8 GPU single pmemd run with amber 16? Chris Neale (Mon Feb 06 2017 - 12:31:12 PST)
- [AMBER] how to solve syntax error issue Ayesha Kanwal (Tue Feb 07 2017 - 02:09:57 PST)
- Re: [AMBER] DFTB3 in Amber is not there, but it may be in gromacs. Markus Kaukonen (Tue Feb 07 2017 - 03:04:17 PST)
- Re: [AMBER] CpHMD – Effect of explicit ions when calculating the pKa of model compounds Eric Lang (Tue Feb 07 2017 - 05:22:16 PST)
- [AMBER] Amber16 -mpt-2.15-gcc/6.1.0-RHEL7.3- compilation error Sudhakar Lakkaraju (Wed Feb 08 2017 - 07:07:58 PST)
- [AMBER] How to download patches and updates manually Elisa Pieri (Wed Feb 08 2017 - 07:49:21 PST)
- [AMBER] VdW parameters in AMBER Andreas Gavrielides (Wed Feb 08 2017 - 08:48:12 PST)
- [AMBER] Failed to calculate entropy with mm_pbsa.pl in AMBER14, with no error informations reported in nmode_com.1.out wei (Wed Feb 08 2017 - 20:36:47 PST)
- [AMBER] CHARMM36 force field Shanghaitech University WuMeng (Thu Feb 09 2017 - 05:08:38 PST)
- [AMBER] PCA analysis Thakur, Abhishek (Thu Feb 09 2017 - 06:58:24 PST)
- [AMBER] Possible BUG in pmemd.cuda - minimization with igb eq 6 Marek Maly (Thu Feb 09 2017 - 07:09:32 PST)
- [AMBER] custom directory for DFTB parameter files Alfredo Quevedo (Thu Feb 09 2017 - 07:41:36 PST)
- [AMBER] Obtain dynamical matrix away from equilibrium The Cromicus Productions (Thu Feb 09 2017 - 10:00:37 PST)
- [AMBER] PCA Thakur, Abhishek (Thu Feb 09 2017 - 14:20:48 PST)
- [AMBER] RE：RE: Failed to calculate entropy with mm_pbsa.pl in AMBER14, with no error informations reported in nmode_com.1.out wei (Thu Feb 09 2017 - 15:48:42 PST)
- [AMBER] Explicity solvent CpHD, -cprestrt .cpin file Tsibela German Tebello Mofokeng (Fri Feb 10 2017 - 06:40:18 PST)
- [AMBER] ZAFF LEAP Carbonic Anhydrase II Protein Topology & Coordinate Preparation Naiem Issa (Fri Feb 10 2017 - 12:43:53 PST)
- Re: [AMBER] Re：Re: RE：RE: Failed to calculate entropy with mm_pbsa.pl in AMBER14, with no error_informations_reported_in_nmode_com.1.out Elvis Martis (Fri Feb 10 2017 - 21:25:07 PST)
- [AMBER] H_bond Thakur, Abhishek (Sun Feb 12 2017 - 08:22:13 PST)
- [AMBER] Compilation errors Sudhakar Lakkaraju (Sun Feb 12 2017 - 18:06:07 PST)
- [AMBER] CPPTRAJ combined clustering with different topologies Jan Ludwiczak (Mon Feb 13 2017 - 04:59:02 PST)
- [AMBER] Should ig value be set explicitly? Azade Yazdan Yar (Mon Feb 13 2017 - 08:17:41 PST)
- [AMBER] Velocity file output AMBER16 Korey M Reid (Mon Feb 13 2017 - 13:14:46 PST)
- [AMBER] production error. Saman Yousuf ali (Mon Feb 13 2017 - 21:37:46 PST)
- [AMBER] Amber Energy Unit Meaning Eugene Cha (Mon Feb 13 2017 - 22:47:34 PST)
- [AMBER] [Amber] Frequencies from normal mode analysis in nab The Cromicus Productions (Tue Feb 14 2017 - 00:03:38 PST)
- [AMBER] PLUMED Meeting 2017 Giovanni Bussi (Tue Feb 14 2017 - 01:03:01 PST)
- Re: [AMBER] pmemd.cuda.MPI not running well with SGE Wang, Yin (Tue Feb 14 2017 - 08:12:15 PST)
- [AMBER] Amber15 Cpinutil.py Bug Chase Zagorec-Marks (Tue Feb 14 2017 - 13:19:09 PST)
- [AMBER] binding free energy- error calculation Mary Varughese (Tue Feb 14 2017 - 21:01:57 PST)
- [AMBER] help in parameters Robin Jain (Tue Feb 14 2017 - 22:08:34 PST)
- [AMBER] building premed for Intel Xeon Phi coprocessors (offload mode) Song-Ho Chong (Tue Feb 14 2017 - 23:04:21 PST)
- [AMBER] constant pH caluculations with pmemd.cuda.MPI Hofer, Florian (Wed Feb 15 2017 - 04:50:44 PST)
- [AMBER] Installation problem with miniconda ABHIJEET CHOWDHURY (Wed Feb 15 2017 - 05:13:36 PST)
- [AMBER] frequency contact maps antonio.coluccia.uniroma1.it (Wed Feb 15 2017 - 06:28:05 PST)
- [AMBER] Hydrophobic and pi-pi interaction Thakur, Abhishek (Wed Feb 15 2017 - 07:40:14 PST)
- [AMBER] Creating a double bond in a pdb file with xleap Aseel Bala (Wed Feb 15 2017 - 11:08:03 PST)
- [AMBER] Simulations with R_OF_GYRATION Osman, Roman (Wed Feb 15 2017 - 11:29:30 PST)
- [AMBER] LES, Umbrella sampling and/or NEB Stregone (Thu Feb 16 2017 - 03:50:59 PST)
- [AMBER] density and concentration of 8Mureabox Jorge Iulek (Thu Feb 16 2017 - 08:44:18 PST)
- [AMBER] Problem using nmropt=1 with CUDA - AMBER 14 Jenner Bonanata (Thu Feb 16 2017 - 09:09:16 PST)
- [AMBER] MMPBSA error konda003 . (Thu Feb 16 2017 - 12:02:35 PST)
- [AMBER] IERR CPU hang needing support please Curtis Walker (Thu Feb 16 2017 - 14:11:17 PST)
- [AMBER] makeDIST_RST issue Miguel Garavís (Fri Feb 17 2017 - 04:29:00 PST)
- [AMBER] LeAP and FFs for Hybrid DNA/RNA structure Kasprzak, Wojciech (NIH/NCI) [C] (Fri Feb 17 2017 - 12:09:39 PST)
- [AMBER] Na cation drifts away from metal chelating protein Michael Shokhen (Sun Feb 19 2017 - 01:45:13 PST)
- [AMBER] Distance between of each residues of two chains within trajectory Jesmita Dhar (Mon Feb 20 2017 - 01:22:33 PST)
- [AMBER] SO4 molecule xleap ARMIN HODAEI (Mon Feb 20 2017 - 02:53:06 PST)
- [AMBER] Problem with mmpbsa Tiffani Rovira (Mon Feb 20 2017 - 04:11:04 PST)
- [AMBER] error in the input file Michael Shokhen (Mon Feb 20 2017 - 04:47:03 PST)
- [AMBER] changing chirality with ParmEd? Thomas Pochapsky (Mon Feb 20 2017 - 07:14:48 PST)
- Re: [AMBER] Using CHARMM 36 force field in AMBER Brian Radak (Mon Feb 20 2017 - 07:55:56 PST)
- [AMBER] 12-6-4 potential in TI Qinghua Liao (Mon Feb 20 2017 - 14:37:24 PST)
- [AMBER] minimization issue (**** in rst file) Chinh Su Tran To (Mon Feb 20 2017 - 19:07:46 PST)
- [AMBER] tleap error Manjula Saravanan (Mon Feb 20 2017 - 22:48:03 PST)
- [AMBER] binding free energy- error calculation doubt Mary Varughese (Tue Feb 21 2017 - 02:08:15 PST)
- Re: [AMBER] AMBER Digest, Vol 1852, Issue 1 Tiffani Rovira (Tue Feb 21 2017 - 02:41:48 PST)
- [AMBER] problem with CpHMD Michael Shokhen (Tue Feb 21 2017 - 04:03:39 PST)
- [AMBER] Memory usage of NMR center of mass restreaints on GPUs paul (Tue Feb 21 2017 - 05:33:15 PST)
- [AMBER] > source leaprc.water.tip3p chemocev marker (Tue Feb 21 2017 - 05:35:57 PST)
- [AMBER] ParmEd problem: LJ12_6_4Error: Could not find parameters for ATOM_TYPE CL 杨金鹏 (Tue Feb 21 2017 - 05:42:20 PST)
- [AMBER] When does cpptraj use information from the original pdb file? Markowska (Tue Feb 21 2017 - 05:54:17 PST)
- [AMBER] Segmentation fault when starting parmchk2 for a modified aminoacid residue Nikolay N. Kuzmich (Tue Feb 21 2017 - 06:03:32 PST)
- [AMBER] antechamber warning Saman Yousuf ali (Tue Feb 21 2017 - 08:16:31 PST)
- [AMBER] AMBER 16 problem with LEaP's addIons command Kasprzak, Wojciech (NIH/NCI) [C] (Tue Feb 21 2017 - 13:20:31 PST)
- [AMBER] antechamber warning Saman Yousuf ali (Tue Feb 21 2017 - 22:18:13 PST)
- [AMBER] Fwd: SQM Error Mitul Srivastava (Tue Feb 21 2017 - 22:53:01 PST)
- [AMBER] Minimisation error and system blowup for a large protein using implicit solvent Joseph Salmon (Wed Feb 22 2017 - 06:54:03 PST)
- [AMBER] problems with heating Alicia Merlino (Wed Feb 22 2017 - 11:24:34 PST)
- [AMBER] Amber force filed parameter Statics Eng (Wed Feb 22 2017 - 14:30:14 PST)
- [AMBER] Antechamber Gaff Am1-bcc charges Neha Gandhi (Thu Feb 23 2017 - 00:22:07 PST)
- [AMBER] This error may be due to faulty Connection atoms when using cationic dummy model JinpengYang (Thu Feb 23 2017 - 03:59:05 PST)
- [AMBER] scale part of the system with Parmed Qinghua Liao (Thu Feb 23 2017 - 04:42:11 PST)
- [AMBER] DIMENSION OF BOX Subashini .K (Thu Feb 23 2017 - 04:58:15 PST)
- [AMBER] pbsa EDISPER with radiopt=0 vs radiopt=1 Paulo Costa (Thu Feb 23 2017 - 06:57:40 PST)
- [AMBER] Sander python API problem (?) Elisa Pieri (Thu Feb 23 2017 - 07:05:15 PST)
- [AMBER] Alternatives to ambmask that might work with parmed/gromber generated .prmtop files? Chris Neale (Thu Feb 23 2017 - 10:13:16 PST)
- [AMBER] pbsa EDISPER with radiopt=0 vs radiopt=1 Paulo Costa (Fri Feb 24 2017 - 01:32:23 PST)
- [AMBER] REMD potential energy fluctuation sarah colin (Fri Feb 24 2017 - 03:18:15 PST)
- [AMBER] Free energy calculation SHAKE's failure when heating. Artem Shekhovtsov (Fri Feb 24 2017 - 08:11:53 PST)
- [AMBER] Charge error in Antechamber. Vatsal Purohit (Fri Feb 24 2017 - 08:50:57 PST)
- [AMBER] Non standrad residue unknown parameters and atomtypes Maral Aminpour (Fri Feb 24 2017 - 09:22:37 PST)
- [AMBER] STRIP Thakur, Abhishek (Fri Feb 24 2017 - 11:36:55 PST)
- [AMBER] pi-pi interaction and hydrophobic Thakur, Abhishek (Fri Feb 24 2017 - 12:59:02 PST)
- [AMBER] How to define a "Dihedral parameters" crossing a C-C triple bond? (Due to two fragment's interaction) Siwei Wang (Fri Feb 24 2017 - 18:32:11 PST)
- [AMBER] Call for awards applications for ACS COMP Division Fall meeting in DC Carlos Simmerling (Sat Feb 25 2017 - 03:08:05 PST)
- Re: [AMBER] [q4md-fft] Unknown parameters frcmod.unknown FyD (Sun Feb 26 2017 - 02:05:02 PST)
- [AMBER] Problems reading in TIP3P parameters Geoffrey Gray (Sun Feb 26 2017 - 09:51:33 PST)
- [AMBER] MM energy contributions of atoms in a molecule Jas Kalayan (Mon Feb 27 2017 - 08:52:51 PST)
- [AMBER] Cannot convert rst to pdb file after md simulation. Vatsal Purohit (Mon Feb 27 2017 - 09:29:13 PST)
- [AMBER] request for input files Adrian Roitberg (Mon Feb 27 2017 - 10:24:56 PST)
- [AMBER] periodic boundary conditions Neha Gandhi (Mon Feb 27 2017 - 17:19:56 PST)
- [AMBER] problem about pressure setting 吴萌 (Mon Feb 27 2017 - 19:40:24 PST)
- [AMBER] cpptraj: dihcovar and projection need trajin to work properly? Thomas Fox (Tue Feb 28 2017 - 07:33:54 PST)
- Last message date: Tue Feb 28 2017 - 11:30:02 PST
- Archived on: Fri Nov 22 2024 - 05:55:24 PST
