Amber Archive Aug 2014 by thread
- Re: [AMBER] this a very green neophyte's question. Parker de Waal (Thu Jul 31 2014 - 20:13:57 PDT)
- Re: [AMBER] HELP Needed: AMBER12 cuda compilation ERROR Saikat Dutta chowdhury (Thu Jul 31 2014 - 23:03:38 PDT)
- [AMBER] what's the difference between imin=1 and imin=5 when performing minimizations on structures from MD trajectory ye renlo (Fri Aug 01 2014 - 01:18:56 PDT)
- Re: [AMBER] question about lipid tutorial Dickson, Callum J (Fri Aug 01 2014 - 04:49:09 PDT)
- [AMBER] parameters for Mutant HP35 NelNel (PDB code 2F4K) Subrata Paul (Fri Aug 01 2014 - 05:42:08 PDT)
- Re: [AMBER] Zinc parameterization Nadia Li (Fri Aug 01 2014 - 10:34:41 PDT)
- [AMBER] AMBER14 Tutorial: Lipid14 Edition Shekter, Lee R (Fri Aug 01 2014 - 11:03:58 PDT)
- [AMBER] Metal parametrization problem!! Pedro A. Baldera Aguayo (Fri Aug 01 2014 - 11:17:24 PDT)
- [AMBER] MM-PBSA ALA scanning module bharat lakhani (Fri Aug 01 2014 - 14:17:36 PDT)
- Re: [AMBER] Problem with atommap in cpptraj Rajeswari A. (Fri Aug 01 2014 - 22:03:23 PDT)
- [AMBER] MMPBSA prmtop problem Nadia Li (Fri Aug 01 2014 - 23:40:59 PDT)
- [AMBER] Script error in Umbrella tutorial Kshatresh Dutta Dubey (Sun Aug 03 2014 - 11:56:46 PDT)
- [AMBER] glycated residue parameter Sangita Kachhap (Sun Aug 03 2014 - 22:10:39 PDT)
- [AMBER] MMPBSA.py -make-mdins does not work with nmode Hiromasa WATANABE (Mon Aug 04 2014 - 03:57:36 PDT)
- Re: [AMBER] ScaledMD for proline dipeptide Niels Geudens (Mon Aug 04 2014 - 05:20:59 PDT)
- [AMBER] Potential Energy is positve for a normal ligand Sun (Mon Aug 04 2014 - 07:49:06 PDT)
- [AMBER] Ptraj cluster error Valentina Romano (Mon Aug 04 2014 - 07:58:42 PDT)
- [AMBER] pmemd.MPI of amber14: run MD twice with the same input but got different output (within statistical error) sun (Mon Aug 04 2014 - 08:39:02 PDT)
- [AMBER] NaN and asterisks error in md.out, and mdinfo files Hoshin Kim (Mon Aug 04 2014 - 12:04:34 PDT)
- [AMBER] mmpbsa on charged sytem Mary Varughese (Tue Aug 05 2014 - 00:19:26 PDT)
- [AMBER] Visualyze avg structure in VMD Valentina Romano (Tue Aug 05 2014 - 03:23:16 PDT)
- [AMBER] Hydrogen bond analysis menwer momo (Tue Aug 05 2014 - 04:45:35 PDT)
- [AMBER] SCF convergence failed during QMMM Muthukumaran R (Tue Aug 05 2014 - 09:23:55 PDT)
- [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Marc van der Kamp (Tue Aug 05 2014 - 09:27:19 PDT)
- [AMBER] Converting (rst) file to PDB using ambpdb menwer momo (Tue Aug 05 2014 - 13:40:11 PDT)
- [AMBER] Memory keyword for QM/MM using ORCA Kshatresh Dutta Dubey (Wed Aug 06 2014 - 00:43:53 PDT)
- [AMBER] help in analysis Robin Jain (Wed Aug 06 2014 - 02:44:16 PDT)
- [AMBER] help in analysis Robin Jain (Wed Aug 06 2014 - 02:44:16 PDT)
- [AMBER] Cluster results Valentina Romano (Wed Aug 06 2014 - 05:22:41 PDT)
- [AMBER] Adding new Bondi radii for mmpbsa Sergey Samsonov (Wed Aug 06 2014 - 07:18:39 PDT)
- [AMBER] Fwd: Unable to generate RESP charges for a charged ligand Manikanthan Bhavaraju (Wed Aug 06 2014 - 07:36:44 PDT)
- [AMBER] SQM error while preparing ATP with antechamber Hirdesh Kumar (Wed Aug 06 2014 - 07:47:54 PDT)
- [AMBER] Questions for pH-REMD by Jason Swails M Olivia Kim (Wed Aug 06 2014 - 10:43:35 PDT)
- [AMBER] Question concerning a torsion parameter Mohammad Salem (Wed Aug 06 2014 - 17:26:29 PDT)
- [AMBER] Percent occupancy of a hydrogen bond menwer momo (Thu Aug 07 2014 - 05:00:46 PDT)
- Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Pablo Ródenas (Thu Aug 07 2014 - 07:54:05 PDT)
- [AMBER] Fwd: problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Sarah Witzke (Thu Aug 07 2014 - 09:11:48 PDT)
- [AMBER] significance of attaching a dummy atom in smd Asmita Gupta (Thu Aug 07 2014 - 10:32:12 PDT)
- [AMBER] unfolding molecule after heating Annika Wittenbecher (Thu Aug 07 2014 - 21:14:51 PDT)
- [AMBER] unfolding molecule after heating Annika Wittenbecher (Thu Aug 07 2014 - 22:16:03 PDT)
- [AMBER] chamber prmtop with changed LJ parameters not accepted by pmemd.cuda? Marc van der Kamp (Fri Aug 08 2014 - 04:12:44 PDT)
- [AMBER] Principal Component/Kullback-Leibler Analysis Jonathan Gough (Fri Aug 08 2014 - 09:17:26 PDT)
- [AMBER] New CPPTRAJ Tutorials Daniel Roe (Fri Aug 08 2014 - 12:49:19 PDT)
- [AMBER] cpptraj.MPI running in 'ensemble' mode. Jonathan Gough (Sat Aug 09 2014 - 11:28:41 PDT)
- [AMBER] Performance of RuBisCo (74, 916) atoms on NVIDIA Tesla K40 GPU Amit Harode (Mon Aug 11 2014 - 05:34:30 PDT)
- [AMBER] Antechamber Error: Cannot open file CORR_NAME_TYPE.DAT, exit Andy Tsai (Mon Aug 11 2014 - 16:41:42 PDT)
- [AMBER] Minimization and equilibration with SANDER.MPI and production with PMEMD.cuda ?? Hirdesh Kumar (Tue Aug 12 2014 - 07:09:58 PDT)
- [AMBER] build branched polymer in leap? Sally Pias (Tue Aug 12 2014 - 16:32:59 PDT)
- [AMBER] error: "STOP PMEMD terminated abnormally" Chinh Su Tran To (Wed Aug 13 2014 - 00:06:48 PDT)
- [AMBER] amber/gaussian find the transition state 王珍 (Wed Aug 13 2014 - 02:03:19 PDT)
- [AMBER] Parameters for ATP and MG2+ Valentina Romano (Wed Aug 13 2014 - 07:56:32 PDT)
- [AMBER] ATP and MG2+prep and frcmod files Valentina Romano (Wed Aug 13 2014 - 08:28:27 PDT)
- [AMBER] Very high values of Diffusion coefficient of water DEBOSTUTI GHOSHDASTIDAR (Wed Aug 13 2014 - 22:09:52 PDT)
- [AMBER] Using polarized force field lead to large RMS in the second step of minimization 张冬冬 (Thu Aug 14 2014 - 02:23:13 PDT)
- [AMBER] Antechamber error Valentina Romano (Thu Aug 14 2014 - 02:38:24 PDT)
- [AMBER] Help on Normal Mode Analysis xy21hb (Thu Aug 14 2014 - 07:55:12 PDT)
- [AMBER] Kinase and ATP MD simulation Valentina Romano (Thu Aug 14 2014 - 08:49:45 PDT)
- [AMBER] Dynamic selection of donor and acceptor mask for hbond analysis DEBOSTUTI GHOSHDASTIDAR (Fri Aug 15 2014 - 03:11:22 PDT)
- [AMBER] errors for surf command in cpptraj Wei Chen (Fri Aug 15 2014 - 09:50:07 PDT)
- [AMBER] restraints with natural language Hugo Azurmendi (Fri Aug 15 2014 - 12:11:21 PDT)
- [AMBER] Calculating electrostatic potential in cpptraj Covington, Cody Lance (Fri Aug 15 2014 - 13:21:41 PDT)
- [AMBER] bad atom type o Hallel Freedman (Sun Aug 17 2014 - 15:42:38 PDT)
- [AMBER] nmode for chamber prmtop Wei Chen (Mon Aug 18 2014 - 07:01:01 PDT)
- [AMBER] QM/MM in Amber Muthukumaran R (Mon Aug 18 2014 - 10:12:00 PDT)
- [AMBER] perl script to convert GIST output to .dx file DEBOSTUTI GHOSHDASTIDAR (Mon Aug 18 2014 - 11:11:13 PDT)
- [AMBER] How to visualize PCA Tamara Meirelles (Mon Aug 18 2014 - 18:08:39 PDT)
- [AMBER] 10 Error on OPEN: ANTECHAMBER.ESP 전선희 (Mon Aug 18 2014 - 23:17:38 PDT)
- [AMBER] Calculating lipid diffusion using mass weighted feature Vijay Manickam Achari (Tue Aug 19 2014 - 00:02:09 PDT)
- [AMBER] principal axes calculation in ptraj Asmita Gupta (Tue Aug 19 2014 - 02:12:48 PDT)
- [AMBER] PCA projection de Manzanos Guinot, Angela (Tue Aug 19 2014 - 02:52:42 PDT)
- [AMBER] ambpdb error Urszula Uciechowska (Tue Aug 19 2014 - 04:01:13 PDT)
- Re: [AMBER] pmemdTI test failure Huang (Tue Aug 19 2014 - 05:15:46 PDT)
- [AMBER] Question on Updating AMBER Gulsevin,Alican (Tue Aug 19 2014 - 05:18:58 PDT)
- [AMBER] puckering of 6 member ring Lara rajam (Tue Aug 19 2014 - 06:06:31 PDT)
- [AMBER] Calculating lipid diffusion Vijyan Achari (Tue Aug 19 2014 - 19:07:36 PDT)
- [AMBER] antechamber 闫玉娜 (Tue Aug 19 2014 - 19:31:10 PDT)
- [AMBER] Problem with Firefly optimisation in R.E.D server George Patargias (Wed Aug 20 2014 - 02:06:44 PDT)
- [AMBER] Contacts Sourav Purohit (Wed Aug 20 2014 - 05:22:07 PDT)
- [AMBER] ATTN NEED REVISION error - reg Radhika Swathi (Wed Aug 20 2014 - 10:49:45 PDT)
- [AMBER] Parametrization of glycerol and desoxycorticosterone BATUHAN KAV (Wed Aug 20 2014 - 10:54:56 PDT)
- [AMBER] Parametrization of glycerol and desoxycorticosterone BATUHAN KAV (Wed Aug 20 2014 - 10:59:16 PDT)
- [AMBER] positive free energy zahra khatti (Wed Aug 20 2014 - 11:11:29 PDT)
- [AMBER] antechamber parametrization of desoxycorticosterone BATUHAN KAV (Thu Aug 21 2014 - 05:59:39 PDT)
- [AMBER] antechamber parametrization of desoxycorticosterone BATUHAN KAV (Thu Aug 21 2014 - 06:14:41 PDT)
- [AMBER] Using iwrap with a dimer Caitlin Scott (Thu Aug 21 2014 - 06:45:28 PDT)
- [AMBER] clustering Lara rajam (Thu Aug 21 2014 - 10:27:07 PDT)
- [AMBER] Using setbox command to prepare files for Umbrella Sampling George Green (Thu Aug 21 2014 - 12:28:45 PDT)
- [AMBER] MCPB and sidechain.bcl problem 高彧辉 (Fri Aug 22 2014 - 05:55:30 PDT)
- [AMBER] Testing of the convergence by means of PCA James Starlight (Fri Aug 22 2014 - 10:00:13 PDT)
- Re: [AMBER] [Private q4md] R.E.D. Server: Private assistance FyD (Fri Aug 22 2014 - 12:27:23 PDT)
- [AMBER] Implicit solvent simulation study Bajarang Kumbhar (Sat Aug 23 2014 - 22:42:54 PDT)
- Re: [AMBER] AMBER Digest, Vol 956, Issue 1 Bajarang Kumbhar (Sun Aug 24 2014 - 23:32:02 PDT)
- [AMBER] Error in making and running xleap ammarah.ghaffar.comsats.edu.pk (Mon Aug 25 2014 - 02:25:46 PDT)
- [AMBER] Implicit solvation method: problem with the rst file M.Venkata Satish Kumar (Mon Aug 25 2014 - 04:08:51 PDT)
- [AMBER] MMPBSA.py -nan values. Dhananjay (Mon Aug 25 2014 - 09:36:58 PDT)
- [AMBER] Undocumented DSSP commands and torsional analysis Eugene Yedvabny (Tue Aug 26 2014 - 00:48:53 PDT)
- [AMBER] Distance command zahra khatti (Tue Aug 26 2014 - 05:30:38 PDT)
- [AMBER] problem in understanding the K+ parameter Indrajit Deb (Tue Aug 26 2014 - 05:34:54 PDT)
- [AMBER] Triply bonded oxygen Gulsevin,Alican (Tue Aug 26 2014 - 15:21:05 PDT)
- [AMBER] Prediction of the protonation state for the ensemble of pdb structures James Starlight (Wed Aug 27 2014 - 00:40:51 PDT)
- [AMBER] Question for residues.py to parameterize a nonstandard residue for constant pH MD M Olivia Kim (Wed Aug 27 2014 - 12:30:20 PDT)
- [AMBER] harmonic restraint Nadia Li (Wed Aug 27 2014 - 17:00:42 PDT)
- [AMBER] antechamber error message 전선희 (Wed Aug 27 2014 - 20:02:13 PDT)
- [AMBER] Error in making and running xleap ammarah.ghaffar.comsats.edu.pk (Thu Aug 28 2014 - 02:52:23 PDT)
- [AMBER] amber 14 tests errors Jordi Bujons (Thu Aug 28 2014 - 11:23:27 PDT)
- [AMBER] system size more than 1000 residues Pengzhi Zhang (Thu Aug 28 2014 - 12:36:12 PDT)
- [AMBER] Mg 12-6-4 potential using parmed Brian Radak (Thu Aug 28 2014 - 12:45:19 PDT)
- [AMBER] On combining different force-fields and charge-derivation methods Mohammad Salem (Thu Aug 28 2014 - 16:27:29 PDT)
- [AMBER] nab Mary Varughese (Fri Aug 29 2014 - 01:56:39 PDT)
- [AMBER] Obtaining representative structures from clustering Jonathan Gough (Fri Aug 29 2014 - 07:56:06 PDT)
- [AMBER] updates about ACPYPE Alan (Sat Aug 30 2014 - 03:41:24 PDT)
- [AMBER] the force constant in umberlla simpling Sun (Sun Aug 31 2014 - 01:35:42 PDT)
- [AMBER] Do the Charmm FF parameters apply to Amber? 张冬冬 (Sun Aug 31 2014 - 08:09:42 PDT)
- Last message date: Sun Aug 31 2014 - 11:00:02 PDT
- Archived on: Fri Nov 22 2024 - 05:54:56 PST
