Amber Archive Nov 2012 by thread
- Re: [AMBER] antechamber limitation on molecule size anyiphysics.gmail.com (Wed Oct 31 2012 - 18:27:50 PDT)
- Re: [AMBER] error when Chamber dealing with DNA, RNA and ATP baogen duan (Wed Oct 31 2012 - 19:40:53 PDT)
- Re: [AMBER] Problem in running parallel hari krishna (Wed Oct 31 2012 - 23:13:52 PDT)
- [AMBER] solvation free enrgy calculation using PB equation. baogen duan (Thu Nov 01 2012 - 01:56:51 PDT)
- [AMBER] metal protein -regarding subramanian boopathi (Thu Nov 01 2012 - 03:49:52 PDT)
- Re: [AMBER] Download problem of amber12 Sanjib Paul (Thu Nov 01 2012 - 03:59:43 PDT)
- [AMBER] Best atom types for N-Oxides compounds like TMAO sa (Thu Nov 01 2012 - 05:39:44 PDT)
- [AMBER] force field file problem Changqing Yan (Thu Nov 01 2012 - 06:16:08 PDT)
- [AMBER] implementation of string method to find minimum free energy paths in Amber Tan Yaw Sing (Thu Nov 01 2012 - 06:49:34 PDT)
- Re: [AMBER] Amber and P450 cytochromes Maximilian Ebert (Thu Nov 01 2012 - 08:25:07 PDT)
- [AMBER] references ? JAIME RUBIO MARTINEZ (Thu Nov 01 2012 - 11:27:40 PDT)
- [AMBER] vlimit exceed for step 1- regarding subramanian boopathi (Thu Nov 01 2012 - 21:55:42 PDT)
- [AMBER] Amber12 PETASCALE Benchmarking. BERGY (Thu Nov 01 2012 - 22:09:02 PDT)
- [AMBER] Cannot setting AMBERHOME on ubuntu 12.04 setyanto md (Fri Nov 02 2012 - 01:14:58 PDT)
- [AMBER] vlimit exceeded error regarding subramanian boopathi (Fri Nov 02 2012 - 08:01:24 PDT)
- [AMBER] how to calculate binding energy of one receptor and two ligands? bin wang (Fri Nov 02 2012 - 08:53:14 PDT)
- Re: [AMBER] Amber12 Parrell Installation Error BERGY (Fri Nov 02 2012 - 10:15:10 PDT)
- Re: [AMBER] deprotonated serine BERGY (Fri Nov 02 2012 - 10:19:27 PDT)
- [AMBER] AMBER-Gaussian and Infrared marawan hussain (Fri Nov 02 2012 - 19:07:05 PDT)
- [AMBER] Problem related to the RMSD Sindrila Dutta banik (Sat Nov 03 2012 - 07:25:11 PDT)
- [AMBER] no leaprc in search path Fabian Glaser (Sun Nov 04 2012 - 06:37:14 PST)
- [AMBER] Problem related to RMSD Sindrila Dutta banik (Sun Nov 04 2012 - 09:43:08 PST)
- [AMBER] MMPBSA.py "timer: need to reset the time before start" Adelene Sim (Sun Nov 04 2012 - 18:51:49 PST)
- [AMBER] Clarifications in umbrella sampling Sajeewa Pemasinghe (Sun Nov 04 2012 - 20:32:22 PST)
- [AMBER] Problem related to the RMSD Sindrila Dutta banik (Sun Nov 04 2012 - 22:37:27 PST)
- [AMBER] How to use q4md-CD? Liu Denis (Mon Nov 05 2012 - 08:07:55 PST)
- [AMBER] workstation . mirage (Mon Nov 05 2012 - 08:45:39 PST)
- [AMBER] tleap not recognizing Na+ David Condon (Mon Nov 05 2012 - 10:23:40 PST)
- Re: [AMBER] [Private q4md] R.E.D. Server: Private assistance FyD (Mon Nov 05 2012 - 12:15:33 PST)
- [AMBER] Dipole from a mask Ismail, Mohd F. (Mon Nov 05 2012 - 13:29:34 PST)
- [AMBER] pmemd cuda MPI nmropt crashes Scott Brozell (Mon Nov 05 2012 - 22:08:45 PST)
- [AMBER] pmemd cuda MPI and PBS_GPUFILE Scott Brozell (Mon Nov 05 2012 - 22:24:45 PST)
- [AMBER] Cannot match namelist object name scee Esam Tolba (Tue Nov 06 2012 - 06:26:47 PST)
- [AMBER] best tutorials Fabian Glaser (Tue Nov 06 2012 - 06:32:26 PST)
- Re: [AMBER] questions about thermodynamic integration atom name and order Yulin Huang (Tue Nov 06 2012 - 07:20:32 PST)
- [AMBER] compiler errors Brown, Paul (Tue Nov 06 2012 - 08:06:04 PST)
- [AMBER] about angle restraint anyiphysics.gmail.com (Tue Nov 06 2012 - 11:53:22 PST)
- [AMBER] Image problems with IWRAP=1 Brown, Kyle (Tue Nov 06 2012 - 11:57:05 PST)
- [AMBER] questions about AMBER prep files Yulin Huang (Tue Nov 06 2012 - 14:14:43 PST)
- [AMBER] error of MMPBSA calculation using the prmtop and inpcrd generated by Chamber program baogen duan (Tue Nov 06 2012 - 18:25:19 PST)
- [AMBER] Energy Analysis from Trajectory Aron Broom (Tue Nov 06 2012 - 22:07:25 PST)
- [AMBER] Umbrella sampling with pmemd Sajeewa Pemasinghe (Tue Nov 06 2012 - 22:59:17 PST)
- [AMBER] Will Ptraj image the coordinates after rms fitting? Alan (Tue Nov 06 2012 - 23:12:13 PST)
- [AMBER] "vlimit exceeded for step ..." during SA protocol Baptiste Legrand (Wed Nov 07 2012 - 01:25:59 PST)
- [AMBER] NAMD failed to read Amber parm file Sneha Menon (Wed Nov 07 2012 - 04:25:36 PST)
- [AMBER] bond missing in phosphate group after antechamber run Krisztina Feher (Wed Nov 07 2012 - 11:00:38 PST)
- [AMBER] problem with Ca2.lib manikanthan bhavaraju (Wed Nov 07 2012 - 11:28:50 PST)
- [AMBER] genMetalFF.sh and getCharges.sh not exist Jia Xu (Wed Nov 07 2012 - 23:17:07 PST)
- [AMBER] Multi-protein simulation in a box Rajeswari A. (Thu Nov 08 2012 - 01:28:04 PST)
- [AMBER] using nudged elastic band method with explicit solvent Tan Yaw Sing (Thu Nov 08 2012 - 02:48:00 PST)
- [AMBER] Parameters for amide bond isosteres Cecilia Lindgren (Thu Nov 08 2012 - 03:49:38 PST)
- [AMBER] Heme iron definition: Atom type missing Maximilian Ebert (Thu Nov 08 2012 - 05:35:28 PST)
- [AMBER] different force fields for different molecules in leap Pecher, Josua (Thu Nov 08 2012 - 08:04:04 PST)
- [AMBER] Primary structur to 3D structure Sindrila Dutta banik (Thu Nov 08 2012 - 11:18:29 PST)
- [AMBER] AmberTools versions Maxier Acosta Santiago (Thu Nov 08 2012 - 12:05:15 PST)
- [AMBER] EHBOND values and RESTRAINT values in mdout file Pyle, Ronald (Thu Nov 08 2012 - 14:55:13 PST)
- [AMBER] Obtain trajectory coordinates from LMOD minimization Sangmin Lee (Thu Nov 08 2012 - 22:23:57 PST)
- [AMBER] No radius found for Mg+ using mm_pbsa.pl script baogen duan (Fri Nov 09 2012 - 01:18:25 PST)
- [AMBER] Error at the end of entropy calculation via MMPBSA.py Miguel Ortiz Lombardía (Fri Nov 09 2012 - 06:31:00 PST)
- [AMBER] Regarding Quadruplex Formation Souvik Sur (Fri Nov 09 2012 - 09:54:17 PST)
- [AMBER] System blows up after several nanoseconds using Amber 12 Sasha Perkins (Fri Nov 09 2012 - 19:19:40 PST)
- [AMBER] Amber Error : Segmentation fault Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Sun Nov 11 2012 - 22:15:16 PST)
- [AMBER] Urgent Faez Iqbal khan (Sun Nov 11 2012 - 23:14:23 PST)
- [AMBER] Generating a solvent Box from organic solvent Mark Zottola (Mon Nov 12 2012 - 16:48:24 PST)
- [AMBER] Tleap crash while loading frcmod Daniel Sindhikara (Mon Nov 12 2012 - 20:25:59 PST)
- [AMBER] imaging namd-generated dcd trajectories with cpptraj Vlad Cojocaru (Tue Nov 13 2012 - 02:00:47 PST)
- [AMBER] problem for lipid GAFF Albert (Tue Nov 13 2012 - 02:18:13 PST)
- [AMBER] NOE calculation Meli Massimiliano (Tue Nov 13 2012 - 02:26:33 PST)
- [AMBER] cppparmstrip command provokes segmentation fault Vlad Cojocaru (Tue Nov 13 2012 - 04:13:55 PST)
- [AMBER] Problem with "make install" after "./configure intel" Su, Shiquan (Tue Nov 13 2012 - 13:16:33 PST)
- Re: [AMBER] Problem with "make install" after "./configure intel" Su, Shiquan (Tue Nov 13 2012 - 13:37:08 PST)
- [AMBER] MM PBSA error calculating entropy Aron Broom (Tue Nov 13 2012 - 13:52:03 PST)
- [AMBER] Regarding RNA Duplex formation Souvik Sur (Tue Nov 13 2012 - 22:50:26 PST)
- [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 8857 FE FE Dmitry Mukha (Wed Nov 14 2012 - 00:52:30 PST)
- [AMBER] Odp: Re: problem for lipid GAFF klechward.wp.pl (Wed Nov 14 2012 - 01:28:19 PST)
- [AMBER] Problem of atom typing for the LYN residue? FyD (Wed Nov 14 2012 - 01:53:46 PST)
- [AMBER] Explicit 1-4 pairs Joakim Jämbeck (Wed Nov 14 2012 - 02:09:39 PST)
- [AMBER] Antechamber and GTP Fernando Martín García (Wed Nov 14 2012 - 02:56:42 PST)
- [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 vojtech.mlynsky.upol.cz (Wed Nov 14 2012 - 03:05:29 PST)
- [AMBER] mmpbsa restart Giulia (Wed Nov 14 2012 - 04:31:18 PST)
- [AMBER] COM removed message and Energy Drift Ismail, Mohd F. (Wed Nov 14 2012 - 12:38:41 PST)
- [AMBER] residuegen Osman, Roman (Wed Nov 14 2012 - 14:59:52 PST)
- [AMBER] AMBER/ORCA marawan hussain (Wed Nov 14 2012 - 19:18:19 PST)
- [AMBER] Error in script file while running mm_pbsa.pl Anogna (Wed Nov 14 2012 - 23:32:20 PST)
- [AMBER] AMBER-ORCA marawan hussain (Wed Nov 14 2012 - 23:51:55 PST)
- [AMBER] very large value of "fglen" and "cglen" during MMPBSA.py calculatio using sander.APBS dbaogen (Thu Nov 15 2012 - 05:13:13 PST)
- [AMBER] AMBER-ORCA-Freq marawan hussain (Thu Nov 15 2012 - 14:13:25 PST)
- [AMBER] Problem with the specification of the bellymask Sajeewa Pemasinghe (Thu Nov 15 2012 - 16:55:38 PST)
- [AMBER] large value of "fglen" and "cglen"of iAPBS initiation during MMPBSA python script calculation baogen duan (Thu Nov 15 2012 - 17:31:18 PST)
- [AMBER] WARNING: a parameter is 0.0 for atom Jacopo Sgrignani (Fri Nov 16 2012 - 01:51:09 PST)
- [AMBER] Theorical ramachandran map/energy map of modified residues Baptiste Legrand (Fri Nov 16 2012 - 09:25:13 PST)
- [AMBER] C-C-N angle parameters for benzonitrile Sharma, Purshotam (Fri Nov 16 2012 - 11:07:48 PST)
- [AMBER] QM/MM bugfix for semiempirical NDDO code available, soon Andreas Goetz (Fri Nov 16 2012 - 17:16:04 PST)
- [AMBER] Antechamber Maxier Acosta Santiago (Sat Nov 17 2012 - 12:06:32 PST)
- Re: [AMBER] questions about Accelerated MD Thomas Evangelidis (Sun Nov 18 2012 - 13:48:51 PST)
- [AMBER] Can I mix Glycam and Gaff in a small molecule? Liu Denis (Sun Nov 18 2012 - 23:01:37 PST)
- [AMBER] Amber radii of ions Devlina Chakravarty (Sun Nov 18 2012 - 23:24:00 PST)
- [AMBER] trajout command in ptraj rahul sarma (Sun Nov 18 2012 - 23:52:48 PST)
- [AMBER] mixing of scaling factor in amber 12 Subrata Paul (Mon Nov 19 2012 - 00:56:58 PST)
- [AMBER] generate rst from mdcrd Yunjie Zhao (Mon Nov 19 2012 - 11:57:04 PST)
- [AMBER] unsubscribe Aust, Susanne (Tue Nov 20 2012 - 01:13:01 PST)
- [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' Thomas Evangelidis (Tue Nov 20 2012 - 01:50:52 PST)
- [AMBER] Magnesium ion (Mg2+) simulation dbaogen (Tue Nov 20 2012 - 18:24:21 PST)
- [AMBER] is AMBER FF good enough for long time scaled MD? Albert (Tue Nov 20 2012 - 23:17:54 PST)
- [AMBER] Ligand appears broken after minimization Jitesh Doshi (Wed Nov 21 2012 - 01:49:15 PST)
- [AMBER] selecting a gpu device in multiple gpu system 홍종희 (Wed Nov 21 2012 - 02:42:38 PST)
- [AMBER] strange deprotonation in QM/MM Jacopo Sgrignani (Wed Nov 21 2012 - 07:17:07 PST)
- [AMBER] Forcefield Maxier Acosta Santiago (Wed Nov 21 2012 - 12:06:12 PST)
- [AMBER] Problem to run sander with more than 60 atom types Elise Duboué-Dijon (Thu Nov 22 2012 - 00:40:12 PST)
- [AMBER] Heating process- amber 8 regarding subramanian boopathi (Thu Nov 22 2012 - 23:04:01 PST)
- [AMBER] GPU and ntpr Fernando Martín García (Fri Nov 23 2012 - 03:14:41 PST)
- [AMBER] INTER-molecular RDF only ? Marek Maly (Fri Nov 23 2012 - 05:22:09 PST)
- Re: [AMBER] Happy Thanksgiving!!!! Eliana Asciutto (Fri Nov 23 2012 - 07:06:34 PST)
- [AMBER] Sorry for the previous email Eliana Asciutto (Fri Nov 23 2012 - 07:33:03 PST)
- [AMBER] What nonbonded interactions cutoff to use in amber. Itamar Kass (Sun Nov 25 2012 - 18:57:38 PST)
- [AMBER] Porcupine_Plots_Script Jia Xu (Mon Nov 26 2012 - 03:17:45 PST)
- [AMBER] definition of receptor_mask and ligand_mask using MMPBSA method dbaogen (Mon Nov 26 2012 - 04:30:09 PST)
- [AMBER] ptraj clustering problem (segmentation fault) adarm.nencki.gov.pl (Mon Nov 26 2012 - 05:25:20 PST)
- Re: [AMBER] [PATCH 1/8] AmberTools: Fix buffer overflows in mdgx, nab and ptraj David A Case (Mon Nov 26 2012 - 05:31:36 PST)
- [AMBER] ptraj grid by center of mass Daniel Álvarez García (Mon Nov 26 2012 - 05:55:01 PST)
- [AMBER] LMOD issues in Amber 12 Sarah Edwards (Mon Nov 26 2012 - 11:05:39 PST)
- [AMBER] calculation of protein-DNA complex structure 丁鹏飞 (Mon Nov 26 2012 - 23:18:23 PST)
- [AMBER] Xleap rotation in mac OS Hirdesh Kumar (Tue Nov 27 2012 - 00:47:51 PST)
- Re: [AMBER] MMPBSA.py - problem with complex.prmtop colvin (Tue Nov 27 2012 - 01:16:44 PST)
- [AMBER] complete bond energy list יוכבד (Tue Nov 27 2012 - 01:23:56 PST)
- [AMBER] Antechamber-- Creating inputs for Ammonium-Borane Ravi Tripathi (Tue Nov 27 2012 - 02:09:31 PST)
- [AMBER] UTP and CTP amber force field parameters dbaogen (Tue Nov 27 2012 - 04:43:54 PST)
- [AMBER] calculate the binding free energy of more than one ligand in MMPBSA Shuyi Cao (Tue Nov 27 2012 - 09:05:28 PST)
- [AMBER] simulation for a protein + ligand system with polarizable force field Jagur Lambix (Tue Nov 27 2012 - 12:44:20 PST)
- [AMBER] Reading DESMOND MD trajectory files in CPPTRAJ... Shashidhar Rao (Tue Nov 27 2012 - 13:14:49 PST)
- [AMBER] Polarizable force field for protein + ligand system Jagur Lambix (Tue Nov 27 2012 - 14:47:01 PST)
- Re: [AMBER] MMPBSA.py - problem with complex.prmtop -rdparm: a parameter array overflowed colvin (Tue Nov 27 2012 - 21:46:11 PST)
- [AMBER] error in heating process subramanian boopathi (Tue Nov 27 2012 - 21:47:54 PST)
- [AMBER] Antechamber - Problem with protonated oxygen Ravi Tripathi (Tue Nov 27 2012 - 21:58:39 PST)
- [AMBER] R.E.D calculation cannot be used for CHARMM FF? Albert (Wed Nov 28 2012 - 00:57:19 PST)
- [AMBER] Calculating volume of the ligand manikanthan bhavaraju (Wed Nov 28 2012 - 06:30:15 PST)
- [AMBER] sander.MPI Fabian Glaser (Wed Nov 28 2012 - 06:30:57 PST)
- [AMBER] Doubt about binding dissociation constant manikanthan bhavaraju (Wed Nov 28 2012 - 10:05:59 PST)
- [AMBER] Amber 12 and PGI compilers >= 12.5 Ben Roberts (Wed Nov 28 2012 - 15:09:23 PST)
- [AMBER] Compiler for Amber12 with GTX680 kurisaki (Thu Nov 29 2012 - 02:46:24 PST)
- [AMBER] Solvation in Amber Ravi Tripathi (Thu Nov 29 2012 - 03:46:42 PST)
- [AMBER] is there a difference between the GTX 680 GPU's Jonathan Gough (Thu Nov 29 2012 - 14:03:34 PST)
- [AMBER] The differences of MMPBSA calculations between AT1.5 and AT12, especially in PBSA solvation model. 徐见容 (Thu Nov 29 2012 - 18:43:05 PST)
- [AMBER] The differences of MMPBSA calculations between AT1.5 andAT12, especially in PBSA solvation model. 徐见容 (Thu Nov 29 2012 - 19:05:52 PST)
- [AMBER] GPU compile TEST does not work. kurisaki (Thu Nov 29 2012 - 21:09:33 PST)
- [AMBER] 回复: Re: The differences of MMPBSA calculations between AT1.5and AT12, especially in PBSA solvation model. 徐见容 (Thu Nov 29 2012 - 22:51:16 PST)
- [AMBER] imaging issues during RMSF Sangeetha B (Fri Nov 30 2012 - 06:16:52 PST)
- [AMBER] problem in loading pdb in xleap Shubhadip Das (Fri Nov 30 2012 - 23:12:53 PST)
- Last message date: Fri Nov 30 2012 - 23:30:03 PST
- Archived on: Wed Oct 30 2024 - 05:54:40 PDT
