Amber Archive Jul 2015 by thread
- Re: [AMBER] Output format in sander Brent Krueger (Tue Jun 30 2015 - 21:38:53 PDT)
- [AMBER] Why the entropy contribution from quasi-harmonic and normal mode methods are so different? wliu (Wed Jul 01 2015 - 02:13:54 PDT)
- Re: [AMBER] Rms fitting to a reference structure with a differnt number atoms to top file George Green (Wed Jul 01 2015 - 02:35:04 PDT)
- Re: [AMBER] Compile Failure David A Case (Wed Jul 01 2015 - 05:41:39 PDT)
- [AMBER] Lipid diffusion in cpptraj Life Sciences Inc (Wed Jul 01 2015 - 07:11:56 PDT)
- [AMBER] leap changes residue order Ignacio Faustino (Wed Jul 01 2015 - 09:04:37 PDT)
- [AMBER] water networks and bridge option of the hbond command in cpptraj Vlad Cojocaru (Wed Jul 01 2015 - 10:44:49 PDT)
- [AMBER] QM/MM Equilibration Troubles Brittany Boykin (Wed Jul 01 2015 - 11:00:11 PDT)
- [AMBER] anisotropic vs. semi-isotropic membrane simulations Naomi Rose Latorraca (Wed Jul 01 2015 - 15:01:51 PDT)
- [AMBER] Ambertools15 installation without Amber ANWESHA SARKAR (Thu Jul 02 2015 - 02:16:42 PDT)
- [AMBER] kclust help Harmeet Kaur (Thu Jul 02 2015 - 05:00:37 PDT)
- Re: [AMBER] folding RNA using SGLD Asmita Gupta (Thu Jul 02 2015 - 05:49:02 PDT)
- [AMBER] another leap inconsistency Hannes Loeffler (Thu Jul 02 2015 - 06:44:03 PDT)
- [AMBER] Chlorophyll A .mol2 file Ofir Tal (Thu Jul 02 2015 - 06:45:12 PDT)
- Re: [AMBER] Cpptraj failure Daniel Roe (Thu Jul 02 2015 - 09:45:37 PDT)
- [AMBER] Cpptraj able to identify coordinates written by VMD? Karl Debiec (Thu Jul 02 2015 - 10:31:48 PDT)
- [AMBER] Regarding melt curve MOHD HOMAIDUR RAHMAN (Thu Jul 02 2015 - 21:16:31 PDT)
- [AMBER] help in make .prepin file Robin Jain (Fri Jul 03 2015 - 00:06:00 PDT)
- [AMBER] How to set interatomic distance restraint? Michael Shokhen (Fri Jul 03 2015 - 00:19:37 PDT)
- [AMBER] Question about AMBER energy decomposition Lee-Ping Wang (Fri Jul 03 2015 - 12:28:53 PDT)
- [AMBER] extract coordinates of a specific atom Morteza Chehel Amirani (Fri Jul 03 2015 - 16:43:20 PDT)
- [AMBER] charmmlipid2amber.py Ramin Ekhteiari (Sat Jul 04 2015 - 11:35:49 PDT)
- [AMBER] NOESY volumes restraints Eugene Sviridov (Mon Jul 06 2015 - 04:08:30 PDT)
- [AMBER] assigning atom type and charge Sanjib Paul (Mon Jul 06 2015 - 04:41:08 PDT)
- [AMBER] PME large NFFT John Dood (Mon Jul 06 2015 - 06:18:47 PDT)
- [AMBER] amber topology file for cytochrome c covalently bond to Heme Shoresh Shafei (Mon Jul 06 2015 - 10:07:58 PDT)
- [AMBER] Reference energies for Explicit solvent CpHMD Arjun Sharma (Mon Jul 06 2015 - 10:33:36 PDT)
- [AMBER] cpptraj: bounds command -> grid Thomas Fox (Tue Jul 07 2015 - 00:10:11 PDT)
- [AMBER] cpptraj: rmsd problem Thomas Fox (Tue Jul 07 2015 - 02:15:34 PDT)
- [AMBER] Lipid linked to a peptide Arnoult, Eric [JRDUS] (Tue Jul 07 2015 - 09:57:48 PDT)
- [AMBER] About python usage in AmberTools Juan Eiros Zamora (Tue Jul 07 2015 - 11:05:23 PDT)
- [AMBER] NumPy Import Error for MCPB.py on Amber15 Eleftherios A P Lambros (Tue Jul 07 2015 - 16:23:54 PDT)
- [AMBER] issue using CUDA+MPI+OpenMP Éric Germaneau (Tue Jul 07 2015 - 23:12:45 PDT)
- [AMBER] Paramentrization of a Uracil base with an O3' terminus deprotonated. giulia palermo (Wed Jul 08 2015 - 01:14:39 PDT)
- [AMBER] help in amber Robin Jain (Wed Jul 08 2015 - 02:31:26 PDT)
- [AMBER] problem in amber Robin Jain (Thu Jul 09 2015 - 00:32:05 PDT)
- [AMBER] Unexpected prochirality change from si to re during MD simulation Michael Shokhen (Thu Jul 09 2015 - 01:28:59 PDT)
- [AMBER] Namdenergy problems with non-standard amino acids Clavel (Thu Jul 09 2015 - 02:34:53 PDT)
- [AMBER] Problem in loading the pdb file Harshala Haldankar (Thu Jul 09 2015 - 03:58:07 PDT)
- [AMBER] parameters dATP Francesca Cardamone (Thu Jul 09 2015 - 06:07:07 PDT)
- [AMBER] articles published for ff14SB and GBneck2 Carlos Simmerling (Thu Jul 09 2015 - 07:03:56 PDT)
- Re: [AMBER] Explicit Solvent Constant pH MD Rahul Ramesh (Thu Jul 09 2015 - 09:42:17 PDT)
- Re: [AMBER] AMBER Digest, Vol 1274, Issue 1 Eleftherios A P Lambros (Thu Jul 09 2015 - 14:16:36 PDT)
- [AMBER] Magnesium in MMGBSA Ahmed Ayoub (Thu Jul 09 2015 - 19:27:53 PDT)
- [AMBER] ESURF term in MMGBSA Ahmed Ayoub (Thu Jul 09 2015 - 19:46:54 PDT)
- [AMBER] Order of the atom in prep ourput of antechamber Nicholus Bhattacharjee (Fri Jul 10 2015 - 01:52:24 PDT)
- [AMBER] problems on amoeba force filed implemented in amber fjliu (Fri Jul 10 2015 - 01:53:01 PDT)
- [AMBER] Changing NMR restraint weights Oliver Grant (Fri Jul 10 2015 - 02:02:29 PDT)
- [AMBER] question about advanced tutorial 3 Mohsen Zakeri (Fri Jul 10 2015 - 03:12:03 PDT)
- [AMBER] FEW tutorial Mohsen Zakeri (Fri Jul 10 2015 - 03:37:43 PDT)
- [AMBER] molecules split apart during MD Lara rajam (Fri Jul 10 2015 - 07:20:43 PDT)
- [AMBER] atom mapping Gard Nelson (Fri Jul 10 2015 - 11:38:40 PDT)
- [AMBER] compare two trajectories Xing (Fri Jul 10 2015 - 12:35:10 PDT)
- [AMBER] FATAL: Atom () does not have a type???? Evans, Shalton (Fri Jul 10 2015 - 13:36:05 PDT)
- [AMBER] About charge derivation for enantiomers Tommaso Casalini (Fri Jul 10 2015 - 13:51:40 PDT)
- [AMBER] pmemd.cuda.MPI error - integer divide by zero Bill Miller III (Fri Jul 10 2015 - 14:36:38 PDT)
- [AMBER] pmemd.cuda implementation of sgld Asmita Gupta (Sat Jul 11 2015 - 00:50:31 PDT)
- [AMBER] About charge derivation for enantiomeric molecules Tommaso Casalini (Sat Jul 11 2015 - 02:30:39 PDT)
- [AMBER] Query about adding hydrogens anu chandra (Sat Jul 11 2015 - 13:08:54 PDT)
- [AMBER] Producing Decoys with AmberTools Mohsen Zakeri (Sun Jul 12 2015 - 12:49:25 PDT)
- [AMBER] Problem in Using the Average Command in Cpptraj Robert Molt (Mon Jul 13 2015 - 08:38:15 PDT)
- [AMBER] Relaxing a heme molecule Amber Maharaj (Mon Jul 13 2015 - 13:02:17 PDT)
- [AMBER] help in making xyz file Robin Jain (Tue Jul 14 2015 - 02:14:01 PDT)
- [AMBER] Accelerated md for protein dna complex with modified residue Muthukumaran R (Tue Jul 14 2015 - 11:05:59 PDT)
- [AMBER] ETOT drift and nscm in NVE for calculation of diffusion CHAMI F. (Tue Jul 14 2015 - 11:13:52 PDT)
- [AMBER] strange output from vacuum minimization Albert (Wed Jul 15 2015 - 01:30:48 PDT)
- [AMBER] MMPBSA.py API quasi-harmonic error D.J. Pattinson (Wed Jul 15 2015 - 01:36:03 PDT)
- [AMBER] MPI compiling failed Albert (Wed Jul 15 2015 - 02:32:11 PDT)
- [AMBER] test failed but still work Albert (Wed Jul 15 2015 - 05:31:47 PDT)
- [AMBER] setting up a MD simulation using AMBER Amber mail (Wed Jul 15 2015 - 06:11:10 PDT)
- [AMBER] NetCDF file Marta Wisniewska (Wed Jul 15 2015 - 07:21:16 PDT)
- [AMBER] Error in writing .lib file Elvis Martis (Wed Jul 15 2015 - 20:13:18 PDT)
- [AMBER] Coordinate resetting (SHAKE) cannot be accomplished Vahid Kshani (Wed Jul 15 2015 - 22:27:59 PDT)
- [AMBER] AMBER error : Coordinate resetting (SHAKE) cannot be accomplish ed MASAOKI FUJII (Thu Jul 16 2015 - 00:37:37 PDT)
- [AMBER] running sgld in explicit solvent Asmita Gupta (Thu Jul 16 2015 - 04:01:48 PDT)
- [AMBER] RESP Fit to Atomic Multipoles Yip Yew Mun (Thu Jul 16 2015 - 08:01:46 PDT)
- Re: [AMBER] svdcmp in sander/ncsu-rmsd.F90 (AmberTools15) is sensitive to higher optimizations, suggest using lapack routine instead David A Case (Thu Jul 16 2015 - 09:30:18 PDT)
- Re: [AMBER] NMR restraints with pmemd.cuda problem Needham, Perri (Thu Jul 16 2015 - 12:34:18 PDT)
- [AMBER] Mutation of a protein residue in TI computation with pmemd.MPI M Olivia Kim (Thu Jul 16 2015 - 15:13:06 PDT)
- [AMBER] MCPB.py ValueError Eleftherios A P Lambros (Thu Jul 16 2015 - 18:48:03 PDT)
- [AMBER] frames in mmpbsa.py Albert (Fri Jul 17 2015 - 03:12:45 PDT)
- [AMBER] Deleting multiple atoms in xleap jacob wick (Fri Jul 17 2015 - 05:32:54 PDT)
- [AMBER] no FINAL_RESULTS_MMPBSA.dat generated Albert (Fri Jul 17 2015 - 05:46:23 PDT)
- [AMBER] countless warnning Albert (Fri Jul 17 2015 - 08:17:10 PDT)
- [AMBER] illegal memory access in amber GPU simulations Latorraca, Naomi Rose (Fri Jul 17 2015 - 19:48:47 PDT)
- [AMBER] Problem in saving parameter/topology and coordinate file. Harshala Haldankar (Fri Jul 17 2015 - 22:44:47 PDT)
- [AMBER] help in resp charge Robin Jain (Sat Jul 18 2015 - 00:16:50 PDT)
- [AMBER] help in box size detremination Robin Jain (Sun Jul 19 2015 - 02:19:04 PDT)
- [AMBER] help in box size determination Robin Jain (Sun Jul 19 2015 - 22:08:33 PDT)
- [AMBER] installation without ambertools Asmita Gupta (Mon Jul 20 2015 - 01:17:03 PDT)
- [AMBER] Distance restraint in AMBER 14 and GPU Lionel Sacconnay (Mon Jul 20 2015 - 02:28:23 PDT)
- [AMBER] incorrect determination of atomic number for atom Cl in tleap Ye Renlo (Mon Jul 20 2015 - 06:32:15 PDT)
- [AMBER] Problem cpptraj Bridging H-Bond analysis Beuerle, Matthias (Mon Jul 20 2015 - 06:52:22 PDT)
- [AMBER] CPPTRAJ - Filtering frames based on lowest of the two RMSD values Stevens, David (Mon Jul 20 2015 - 15:30:00 PDT)
- [AMBER] Gaff Parameters Si Sharapa (Mon Jul 20 2015 - 16:08:47 PDT)
- [AMBER] GTX980Ti's now supported for AMBER and Exxact GTX780Tis available at discounted prices Ross Walker (Mon Jul 20 2015 - 17:16:54 PDT)
- [AMBER] MCPB.py Value / Syntax error Eleftherios A P Lambros (Mon Jul 20 2015 - 18:13:25 PDT)
- [AMBER] qm-mmgbsa error Ayesha Fatima (Mon Jul 20 2015 - 21:55:17 PDT)
- Re: [AMBER] Immediate Postdoctoral Position Opening In Dr. Khaled Barakat’s Lab, Faculty Of Pharmacy, University Of Alberta Ayesha Fatima (Tue Jul 21 2015 - 00:26:02 PDT)
- [AMBER] Unchanged coordinates in leap mish (Tue Jul 21 2015 - 02:13:07 PDT)
- [AMBER] PCA and motions visualization antonio.coluccia.uniroma1.it (Tue Jul 21 2015 - 02:59:54 PDT)
- [AMBER] "nstlim" is not reflected correctly in REMD with pmemd.MPI kurisaki (Tue Jul 21 2015 - 04:16:30 PDT)
- [AMBER] MCPB.py N terminal error Jon Uranga (Tue Jul 21 2015 - 06:21:52 PDT)
- [AMBER] Testing the titratable group definition CpHMD Arjun Sharma (Tue Jul 21 2015 - 08:22:55 PDT)
- [AMBER] hbond cpptraj Lara rajam (Tue Jul 21 2015 - 08:26:31 PDT)
- [AMBER] Error in loading inpcrd file in sander Mohsen Zakeri (Tue Jul 21 2015 - 14:29:25 PDT)
- Re: [AMBER] CpptrajPairDist bharat lakhani (Tue Jul 21 2015 - 19:50:08 PDT)
- [AMBER] QM/GBSA calculation failed Albert (Wed Jul 22 2015 - 00:25:17 PDT)
- [AMBER] Periodic Box Size and Charge Determination Aronica, Pietro (Wed Jul 22 2015 - 04:31:11 PDT)
- [AMBER] Explicit solvent pH-REMD whb (Wed Jul 22 2015 - 07:33:14 PDT)
- [AMBER] [cpptraj] Nativecontacts failing with long trajectory Juan Eiros Zamora (Wed Jul 22 2015 - 12:36:08 PDT)
- Re: [AMBER] Monitoring GPU voltage Tru Huynh (Wed Jul 22 2015 - 12:52:30 PDT)
- [AMBER] Amber for phophorylated residue Ziba Bahadori (Thu Jul 23 2015 - 03:12:19 PDT)
- [AMBER] GTX Titan Xs slowing down after 200ns Mohamed Faizan Momin (Thu Jul 23 2015 - 07:12:37 PDT)
- [AMBER] Using TIP4PEW amber FF in NAMD peter.schmidtke.discngine.servier.com (Fri Jul 24 2015 - 01:27:34 PDT)
- [AMBER] MPI_ABORT error Amber mail (Fri Jul 24 2015 - 05:28:02 PDT)
- [AMBER] impose restraint mask for specific residues Latorraca, Naomi Rose (Fri Jul 24 2015 - 11:09:02 PDT)
- [AMBER] Speed of heating MD Amber mail (Sat Jul 25 2015 - 02:32:33 PDT)
- [AMBER] GPU EVGA GTX 980 SC ACX M. Reza Ganjalikhany (Sat Jul 25 2015 - 04:48:36 PDT)
- [AMBER] MD simulation: cis isomer of peptide bond Michael Shokhen (Sun Jul 26 2015 - 09:07:07 PDT)
- [AMBER] strange pbsa results Albert (Mon Jul 27 2015 - 02:54:45 PDT)
- [AMBER] Targeted Molecular dynamics in Amber ROOPALI VERMA (Mon Jul 27 2015 - 03:00:43 PDT)
- [AMBER] detecting and removing corrupted frames Thomas Evangelidis (Mon Jul 27 2015 - 03:32:23 PDT)
- [AMBER] which solvent model to use with solvateCap peter.schmidtke.discngine.servier.com (Mon Jul 27 2015 - 04:12:18 PDT)
- [AMBER] How to combine distance and torsion restraint? Michael Shokhen (Mon Jul 27 2015 - 06:16:30 PDT)
- [AMBER] Prep file for chiral position Nicholus Bhattacharjee (Mon Jul 27 2015 - 09:51:56 PDT)
- [AMBER] MCPB.py mismatch error Eleftherios A P Lambros (Mon Jul 27 2015 - 12:36:35 PDT)
- [AMBER] Cluster restraints Damiano Spadoni (Tue Jul 28 2015 - 09:24:39 PDT)
- [AMBER] Restart of MMPBSA Osman, Roman (Tue Jul 28 2015 - 11:09:29 PDT)
- [AMBER] Issues with running simulation after ParmEd conversion Rohith Mohan (Tue Jul 28 2015 - 16:30:26 PDT)
- [AMBER] MM-GBSA at different temperature Shruti Koulgi (Tue Jul 28 2015 - 23:02:00 PDT)
- [AMBER] Utilization of 3 GPUs suddenly drop to 0% and won't work any more 浅井 賢 (Tue Jul 28 2015 - 23:35:38 PDT)
- [AMBER] how to center on ligand? Albert (Wed Jul 29 2015 - 07:25:35 PDT)
- Re: [AMBER] cpptraj Help rmsd between two homologous proteins and their Trajectory bharat lakhani (Wed Jul 29 2015 - 19:47:32 PDT)
- [AMBER] Antechamber for boronic acid derivatives? Michael Shokhen (Thu Jul 30 2015 - 00:19:17 PDT)
- Re: [AMBER] Fwd: NMR restraints with pmemd.cuda problem Miroslav Krepl (Thu Jul 30 2015 - 02:43:04 PDT)
- [AMBER] Solvents that are not in a list. Sharapa (Thu Jul 30 2015 - 04:16:55 PDT)
- [AMBER] multiple cpus per single gpu job Meij, Henk (Thu Jul 30 2015 - 08:11:13 PDT)
- [AMBER] Explicit-solvent-pH-REMD whb (Fri Jul 31 2015 - 00:48:28 PDT)
- [AMBER] Regarding ADP molecule force fields Yogeeshwar Ajjugal (Fri Jul 31 2015 - 02:41:24 PDT)
- [AMBER] mdfrc units Georgios Gerogiokas (Fri Jul 31 2015 - 06:41:04 PDT)
- Last message date: Fri Jul 31 2015 - 14:00:05 PDT
- Archived on: Fri Dec 20 2024 - 05:55:14 PST
