Amber Archive May 2009 by thread
- RE: [Subject Filtered] [AMBER] hbond-error in amber9 8% Hopkins, Robert (Thu Apr 30 2009 - 17:02:34 PDT)
- Re: [AMBER] Influence about HIS-HIE-HIS-HIP Rilei Yu (Thu Apr 30 2009 - 17:37:17 PDT)
- Re: [AMBER] Amber FF and Glycam Hannes Loeffler (Fri May 01 2009 - 01:33:34 PDT)
- [AMBER] unable to start xleap Jayalakshmi Sridhar (Fri May 01 2009 - 11:32:27 PDT)
- [AMBER] charge of Fe-heme 董昊 (Fri May 01 2009 - 12:08:12 PDT)
- [AMBER] how to assign radii parameters to certain atoms when fitting RESP charge using antechamber Ye MEI (Sat May 02 2009 - 05:00:06 PDT)
- [AMBER] how to assign radii parameters to certain atoms when fitting RESP charge using antechamber Ye MEI (Sat May 02 2009 - 05:01:20 PDT)
- Re: [AMBER] chain restrain x TI Josmar R. da Rocha (Sat May 02 2009 - 10:09:53 PDT)
- [AMBER] equilibration stops for dimer simulation with REMD Sunita Patel (Sat May 02 2009 - 13:11:48 PDT)
- [AMBER] QM/MM assigns Cd to C, Se to S C Liu (Sat May 02 2009 - 19:09:27 PDT)
- [AMBER] LCPO or Molsurf? Dong Xu (Sat May 02 2009 - 20:14:55 PDT)
- [AMBER] High energy during minimization aneesh cna (Sat May 02 2009 - 21:26:16 PDT)
- [AMBER] help with RESP tutorial using antechamber and gaussian Josmar R. da Rocha (Sun May 03 2009 - 10:59:23 PDT)
- [AMBER] make test.parallel.MM error Collins Nganou (Sun May 03 2009 - 14:20:51 PDT)
- [AMBER] prmtop Mark M Huntress (Sun May 03 2009 - 16:20:39 PDT)
- [AMBER] problem with cutoff Yunjie Zhao (Sun May 03 2009 - 20:53:00 PDT)
- [AMBER] "Parameter file not generated" Remya S R (Sun May 03 2009 - 23:17:23 PDT)
- [AMBER] Parameter file not saved Remya S R (Sun May 03 2009 - 23:30:19 PDT)
- [AMBER] creating new residue adds none wanted ter Jorgen Simonsen (Mon May 04 2009 - 00:49:47 PDT)
- [AMBER] MM_PBSA problem in Amber 9 Sean Zhao (Mon May 04 2009 - 02:09:14 PDT)
- [AMBER] Script for parallel runs Catein Catherine (Mon May 04 2009 - 02:17:42 PDT)
- [AMBER] Non-zero internal energy in single trajectory MM-PBSA calculations Dmitry Osolodkin (Mon May 04 2009 - 02:24:59 PDT)
- [AMBER] normal mode analysis Hannes Wallnoefer (Mon May 04 2009 - 02:39:16 PDT)
- [AMBER] Parameter file not saved Remya S R (Mon May 04 2009 - 05:03:08 PDT)
- [AMBER] MMPBSA- interaction energy for every frame Jack Colis (Mon May 04 2009 - 07:38:38 PDT)
- [AMBER] QM/MM Syed Tarique Moin (Mon May 04 2009 - 08:32:29 PDT)
- [AMBER] xleap segmentation fault Jayalakshmi Sridhar (Mon May 04 2009 - 08:50:06 PDT)
- [AMBER] Error in PMEMD run Marek Malý (Mon May 04 2009 - 18:23:33 PDT)
- [AMBER] A confusion about tutorial B1 Houyang Chen (Mon May 04 2009 - 22:01:31 PDT)
- [AMBER] Problem in production run nicholus bhattacharjee (Mon May 04 2009 - 22:50:07 PDT)
- [AMBER] Suggestion for restraining chain of a protein nicholus bhattacharjee (Mon May 04 2009 - 23:29:54 PDT)
- Re: [AMBER] pmemd compilation error john smith (Tue May 05 2009 - 04:20:08 PDT)
- [AMBER] Charge problem Remya S R (Tue May 05 2009 - 04:43:47 PDT)
- [AMBER] Problems with PMEMD installation for AMBER10 German Erlenkamp (Tue May 05 2009 - 05:40:56 PDT)
- [AMBER] skip parallel test Collins Nganou (Tue May 05 2009 - 06:09:00 PDT)
- [AMBER] Can bond clevage & formation conducted by qm/mm via sander? sychen (Tue May 05 2009 - 06:12:32 PDT)
- [AMBER] Error: cannot run prepgen Rose Tamil (Tue May 05 2009 - 08:20:52 PDT)
- [AMBER] difference in temperature Naser Alijabbari (Tue May 05 2009 - 17:02:28 PDT)
- [AMBER] ntf, ntc with softcore potentials and TI in amber10 Matthew Wilce (Tue May 05 2009 - 18:33:28 PDT)
- [AMBER] Error in MM PBSA Vikas Sharma (Wed May 06 2009 - 01:35:57 PDT)
- [AMBER] Conformation of sulfated Glucosamine Neha Gandhi (Wed May 06 2009 - 02:54:31 PDT)
- [AMBER] positive value of binding enrgy after MM PBSA Vikas Sharma (Wed May 06 2009 - 08:07:03 PDT)
- [AMBER] xleap input pdb problem Majeed Shaik (Wed May 06 2009 - 11:47:45 PDT)
- [AMBER] multiple chain specification in Sander Siddharth Rastogi (Wed May 06 2009 - 20:17:57 PDT)
- [AMBER] ptraj PCA - Highest Eigenvalues or First 2 Calculated? Patrick Gedeon (Wed May 06 2009 - 21:12:39 PDT)
- [AMBER] Error in binding energy (MM PBSA) Vikas Sharma (Wed May 06 2009 - 22:47:33 PDT)
- [AMBER] free enrgy error in MM PBSA Vikas Sharma (Thu May 07 2009 - 03:11:44 PDT)
- [AMBER] ambertools for NAMD Jorgen Simonsen (Thu May 07 2009 - 05:35:24 PDT)
- [AMBER] dftb_disper problem Fernando Martín García (Thu May 07 2009 - 05:30:25 PDT)
- [AMBER] Problems in the result of MM_PBSA Sean Zhao (Thu May 07 2009 - 18:30:24 PDT)
- [AMBER] RE: Listing gaff parameters in frcmod Bokun Cho (Thu May 07 2009 - 21:20:46 PDT)
- [AMBER] Error in binding energy (MM PBSA) Vikas Sharma (Thu May 07 2009 - 23:44:33 PDT)
- [AMBER] Re: Marek Malý (Fri May 08 2009 - 12:12:39 PDT)
- [AMBER] Can I use only a single point calculation to derive RESP charges? Josmar R. da Rocha (Fri May 08 2009 - 17:08:54 PDT)
- [AMBER] Modifying a water molecule Jorgen Simonsen (Sat May 09 2009 - 06:16:54 PDT)
- [AMBER] AMBER 94 Charges for terminal LYN, GLH, ASH and CYM residues and some other unusual cases. todd.semichem.com (Sat May 09 2009 - 09:27:52 PDT)
- [AMBER] molsurf and probe radius David Watson (Sat May 09 2009 - 10:32:43 PDT)
- [AMBER] xleap, mac number problem Mark M Huntress (Sat May 09 2009 - 12:46:46 PDT)
- [AMBER] please help me out Nancy (Sun May 10 2009 - 00:56:33 PDT)
- [AMBER] MM-PBSA statistics Musa Ozboyaci (Sun May 10 2009 - 03:00:19 PDT)
- [AMBER] The resonable way to create single strand DNA with NAB ? Marek Malý (Sun May 10 2009 - 10:12:09 PDT)
- [AMBER] building quadruplex with NAB Peter Varnai (Sun May 10 2009 - 16:27:38 PDT)
- [AMBER] Adding non standard residues Jorgen Simonsen (Mon May 11 2009 - 01:54:25 PDT)
- [AMBER] molecular crystal simulation Simona Irrera (Tue May 12 2009 - 04:04:26 PDT)
- [AMBER] ptraj netcdf Bala subramanian (Tue May 12 2009 - 05:04:00 PDT)
- [AMBER] anal output: Entalphy or Free Energy? Edward M (Tue May 12 2009 - 17:14:37 PDT)
- [AMBER] Question about Thermal Integration with Softcore Elodie Laine (Wed May 13 2009 - 02:13:22 PDT)
- [AMBER] amber9 in fedora10 Bala subramanian (Wed May 13 2009 - 02:50:25 PDT)
- [AMBER] ongoing issues using sander with AMOEBA Tomasio, Susana (Wed May 13 2009 - 03:00:00 PDT)
- [AMBER] essential dynamics Chunliyan (Wed May 13 2009 - 09:23:23 PDT)
- [AMBER] re: essential dynamics Chunliyan (Wed May 13 2009 - 10:25:57 PDT)
- [AMBER] normal modes calculation Neha Gandhi (Wed May 13 2009 - 20:12:13 PDT)
- [AMBER] Amber - Leap- SolvateBox help Shubhra Gupta (Wed May 13 2009 - 22:04:16 PDT)
- [AMBER] pmemd running very slow in amber10 Vijay Manickam Achari (Wed May 13 2009 - 22:41:40 PDT)
- Re: [OFFLIST] Re: [AMBER] amber9 in fedora10 Bala subramanian (Thu May 14 2009 - 01:18:07 PDT)
- [AMBER] MM-PBSA tutorial Workalemhu Berhanu (Thu May 14 2009 - 10:16:55 PDT)
- [AMBER] xmin Peter Varnai (Thu May 14 2009 - 14:29:09 PDT)
- [AMBER] MM-PBSA with explicit water mathew k varghese (Thu May 14 2009 - 23:45:23 PDT)
- [AMBER] xleap reading hydrogens giving error Jorgen Simonsen (Fri May 15 2009 - 00:47:10 PDT)
- [AMBER] Fw: MM-PBSA with explicit water mathew k varghese (Thu May 14 2009 - 23:43:46 PDT)
- [AMBER] scee term Neha Gandhi (Fri May 15 2009 - 02:03:48 PDT)
- [AMBER] adding a standard amino acid as ligand sheerychen (Fri May 15 2009 - 02:37:51 PDT)
- [AMBER] secstruct with ptraj Bala subramanian (Fri May 15 2009 - 03:19:54 PDT)
- [AMBER] Issue related to vector saving S.Sundar Raman (Fri May 15 2009 - 06:35:01 PDT)
- [AMBER] MM-GBSA energy decomposition and pairwise decomposition question Dong Xu (Fri May 15 2009 - 15:05:52 PDT)
- [AMBER] FE: unexpected coordination 4 - using nonstandard tree type '4' ben rodriguez (Fri May 15 2009 - 15:09:44 PDT)
- [AMBER] Alignment of small molecule on peptide fragment Workalemhu Berhanu (Sat May 16 2009 - 02:31:08 PDT)
- [AMBER] Alignment of small molecule on peptide fragment Workalemhu Berhanu (Sat May 16 2009 - 02:32:38 PDT)
- [AMBER] Issue related to saving the vector in ptraj S.Sundar Raman (Sat May 16 2009 - 05:41:10 PDT)
- [AMBER] Amber 10 install parallel problem Hopkins, Robert (Sat May 16 2009 - 17:38:16 PDT)
- [AMBER] Running PTRAJ command line scripts in background Hopkins, Robert (Sat May 16 2009 - 17:47:38 PDT)
- [AMBER] makeDIST_RST: no map function for ambiguous restraint Peter Varnai (Sun May 17 2009 - 11:41:24 PDT)
- [AMBER] parallel amber on cluster Siavoush Dastmalchi (Sun May 17 2009 - 23:04:58 PDT)
- [AMBER] Problem in Nmode Kshatresh Dutta Dubey (Sun May 17 2009 - 23:07:52 PDT)
- [AMBER] Modification of His Jorgen Simonsen (Mon May 18 2009 - 03:51:50 PDT)
- [AMBER] Error running MM _PBSA.pl script Vikas Sharma (Mon May 18 2009 - 05:00:13 PDT)
- [AMBER] problem with parmchk rebeca (Mon May 18 2009 - 06:59:51 PDT)
- [AMBER] no equilibrium Nancy (Mon May 18 2009 - 19:32:01 PDT)
- [AMBER] no equilibrium Nancy (Mon May 18 2009 - 19:44:03 PDT)
- [AMBER] The largest AMBER calculation(s)? Vlad (Mon May 18 2009 - 19:58:27 PDT)
- [AMBER] Problem with Nmode Kshatresh Dutta Dubey (Mon May 18 2009 - 21:25:05 PDT)
- [AMBER] AMBER 10 output Sergey Samsonov (Tue May 19 2009 - 00:33:21 PDT)
- [AMBER] Problem with nonstandard residues moitrayee.mbu.iisc.ernet.in (Tue May 19 2009 - 04:48:33 PDT)
- [AMBER] gaff and aromatic compounds rebeca (Tue May 19 2009 - 08:50:02 PDT)
- [AMBER] loadpdb atom type Mark M Huntress (Tue May 19 2009 - 09:20:20 PDT)
- [AMBER] Tutorial A1 Workalemhu Berhanu (Tue May 19 2009 - 16:05:15 PDT)
- [AMBER] resp charge R. A. (Tue May 19 2009 - 19:35:25 PDT)
- [AMBER] gaff and aromatic compounds rebeca (Wed May 20 2009 - 01:54:43 PDT)
- [AMBER] MM PBSA output Vikas Sharma (Wed May 20 2009 - 04:53:57 PDT)
- [AMBER] Amber/CHARMM summer school David A. Case (Wed May 20 2009 - 05:40:39 PDT)
- [AMBER] ptraj questions Jia Xu (Wed May 20 2009 - 07:39:13 PDT)
- [AMBER] RE: add magnesium Ross Walker (Wed May 20 2009 - 14:30:09 PDT)
- [AMBER] how to use two dimensions periodic boundary ? Nancy (Wed May 20 2009 - 18:32:50 PDT)
- [AMBER] errors when add ions zgong.hust (Wed May 20 2009 - 19:51:48 PDT)
- [AMBER] Protein with HETATM, am I doing the nicholus bhattacharjee (Wed May 20 2009 - 21:48:42 PDT)
- [AMBER] Radius for Bromine in MMPBSA calculation john smith (Wed May 20 2009 - 22:24:05 PDT)
- [AMBER] Protein with HETATM, am I doing the right thing nicholus bhattacharjee (Thu May 21 2009 - 04:21:15 PDT)
- [AMBER] Loading PDB of complex Vikas Sharma (Thu May 21 2009 - 06:13:36 PDT)
- [AMBER] Installation directory Thomas Spraggins (Thu May 21 2009 - 11:02:59 PDT)
- [AMBER] Segmentation error in Ptraj Kshatresh Dutta Dubey (Fri May 22 2009 - 00:17:27 PDT)
- [AMBER] lipid membrane(dppc) in amber xueqin pang (Fri May 22 2009 - 01:42:54 PDT)
- [AMBER] lipid membrane(dppc) in amber xueqin pang (Fri May 22 2009 - 02:01:26 PDT)
- [AMBER] decomposition and alanine scanning 廖青华 (Fri May 22 2009 - 07:13:49 PDT)
- [AMBER] MMPBSA extract coordinate vijayaraj.clri.res.in (Fri May 22 2009 - 11:00:57 PDT)
- [AMBER] Nab units ? Marek Maly (Fri May 22 2009 - 17:20:14 PDT)
- [AMBER] 2 atoms not in residue template Workalemhu Berhanu (Sat May 23 2009 - 17:11:12 PDT)
- [AMBER] file contains 2 atoms not in residue templates Workalemhu Berhanu (Sat May 23 2009 - 17:17:09 PDT)
- [AMBER] problem with MM-PBSA Maryam Hamzehee (Sat May 23 2009 - 21:48:05 PDT)
- [AMBER] nanoseconds of simulation with nscm=0 Naser Alijabbari (Sun May 24 2009 - 10:20:18 PDT)
- [AMBER] Unit 8 Error on OPEN: prmtop Workalemhu Berhanu (Sun May 24 2009 - 10:27:38 PDT)
- [AMBER] Strange high temperature in softcore TI Tom Joseph (Sun May 24 2009 - 18:54:43 PDT)
- [AMBER] How to know that the md is stable in equilibration run nicholus bhattacharjee (Mon May 25 2009 - 04:54:25 PDT)
- [AMBER] Problem with MM-PBSA energy calculation Rubben Torella (Mon May 25 2009 - 08:58:41 PDT)
- [AMBER] Question about &dipoles printing in AMBER 8 Karen Callahan (Mon May 25 2009 - 16:46:00 PDT)
- [AMBER] partial charge and topology of intrastrand cross-link DNA Shuang Ding (Mon May 25 2009 - 19:27:43 PDT)
- [AMBER] problem with MM-PBSA Maryam Hamzehee (Mon May 25 2009 - 21:52:29 PDT)
- [AMBER] Molecular simulation of a protein using special H2O cluster Rilei Yu (Tue May 26 2009 - 01:20:56 PDT)
- [AMBER] Re: About Amber installations Alan (Tue May 26 2009 - 02:53:37 PDT)
- [AMBER] ligand QM/semi-empirical coords optmisation Alan (Tue May 26 2009 - 03:55:09 PDT)
- [AMBER] problem with program anal within Amber10 Marina Grabar (Tue May 26 2009 - 04:48:38 PDT)
- [AMBER] partial charges of lipid membrane for GPCR system xueqin pang (Tue May 26 2009 - 06:34:34 PDT)
- [AMBER] mdfil: Error unknown flag during sander minimization Workalemhu Berhanu (Tue May 26 2009 - 06:57:29 PDT)
- [AMBER] RE: About Amber10 installation "Possible Failure" Ross Walker (Tue May 26 2009 - 08:38:19 PDT)
- [AMBER] get typeid of -1, sleap - AMBER with amoeba ff Tomasio, Susana (Tue May 26 2009 - 08:51:18 PDT)
- [AMBER] Tutorial 4 Please check the total charge and your -nc flag Workalemhu Berhanu (Tue May 26 2009 - 12:47:07 PDT)
- [AMBER] FATAL error in creating topology and coordinate files for organic molecules with Antechamber Workalemhu Berhanu (Tue May 26 2009 - 14:45:55 PDT)
- [AMBER] Re: Help with xleap Taufik Al-Sarraj (Tue May 26 2009 - 16:58:00 PDT)
- [AMBER] ACE residue - amoeba_amino.off and amoeba_aminont.off - different labels Tomasio, Susana (Wed May 27 2009 - 04:25:35 PDT)
- RE: [AMBER] ACE residue - amoeba_amino.off and amoeba_aminont.off- different labels Tomasio, Susana (Wed May 27 2009 - 05:13:58 PDT)
- [AMBER] PARMCAL calculation ? Marek Maly (Wed May 27 2009 - 07:19:48 PDT)
- [AMBER] MM-PBSA and NetCDF Bradshaw, Richard (Wed May 27 2009 - 08:38:13 PDT)
- [AMBER] Tutorial 4 Parameter file was not saved Workalemhu Berhanu (Wed May 27 2009 - 09:00:30 PDT)
- [AMBER] heating advice Mark M Huntress (Wed May 27 2009 - 13:44:26 PDT)
- Re: [AMBER] hbond_ptraj Thomas Cheatham (Wed May 27 2009 - 17:39:15 PDT)
- [AMBER] SANDER BOMB PRADEEP VENKATARAMAN (Wed May 27 2009 - 19:39:56 PDT)
- [AMBER] Changing bond length manoj singh (Wed May 27 2009 - 20:47:52 PDT)
- [AMBER] AMOEBA and carbon nanotubes + include parameters Tomasio, Susana (Thu May 28 2009 - 03:23:00 PDT)
- [AMBER] MM-PBSA nmode statistics Dmitry Osolodkin (Thu May 28 2009 - 04:54:18 PDT)
- [AMBER] contacts in ptraj 欧阳德方 (Thu May 28 2009 - 04:55:28 PDT)
- [AMBER] how to know that adequate equilibration from rmsd curve of equilibration nicholus bhattacharjee (Thu May 28 2009 - 06:37:29 PDT)
- [AMBER] FW: About Amber10 installation "Possible Failure" Ross Walker (Thu May 28 2009 - 07:06:31 PDT)
- Re: [AMBER] Minimization error on protonated system? Please help. Thanks! David A. Case (Thu May 28 2009 - 08:17:59 PDT)
- [AMBER] Minimization on MM-PBSA Rubben Torella (Thu May 28 2009 - 08:23:07 PDT)
- [AMBER] xleap segmentation fault Jayalakshmi Sridhar (Thu May 28 2009 - 09:29:47 PDT)
- [AMBER] ask for parm99MOD xiaoqin huang (Thu May 28 2009 - 11:16:35 PDT)
- Re: [AMBER] unnatural amino acid FyD (Thu May 28 2009 - 11:46:27 PDT)
- [AMBER] How to take into account the charge in GAFF parameterization Workalemhu Berhanu (Thu May 28 2009 - 16:22:07 PDT)
- [AMBER] J coupling constant calculation Neha Gandhi (Thu May 28 2009 - 22:24:37 PDT)
- [AMBER] broken Ligand Shubhra Gupta (Fri May 29 2009 - 06:28:22 PDT)
- [AMBER] QQD psuedoatom restraints Titus, Jamie (bairdje) (Fri May 29 2009 - 07:02:31 PDT)
- [AMBER] Targeted MD and QM/MM Gabriel Urquiza (Fri May 29 2009 - 13:09:31 PDT)
- [AMBER] the atom number exceeds the MAXATOM, reallocate memory automatically Workalemhu Berhanu (Sat May 30 2009 - 04:20:03 PDT)
- [AMBER] ERROR in ptrajInitializeState(): Attempting .... Siavoush Dastmalchi (Sat May 30 2009 - 09:06:51 PDT)
- [AMBER] RE: ERROR in ptrajInitializeState(): Attempting .... Siavoush Dastmalchi (Sat May 30 2009 - 10:11:55 PDT)
- [AMBER] Parameter file content manoj singh (Sat May 30 2009 - 18:53:37 PDT)
- [AMBER] create a simulation box Workalemhu Berhanu (Sat May 30 2009 - 20:06:24 PDT)
- [AMBER] can I get partial charge for lipid membrane with Antechamber and RESP xueqin pang (Sun May 31 2009 - 05:43:09 PDT)
- [AMBER] Can we use GROMACS or NAMD for MD, and then use MM-PBSA to culculate binding energy xueqin pang (Sun May 31 2009 - 05:47:57 PDT)
- [AMBER] solutes in a simulation box Workalemhu Berhanu (Sun May 31 2009 - 09:59:39 PDT)
- [AMBER] Choice of force feild manoj singh (Sun May 31 2009 - 10:12:23 PDT)
- [AMBER] Choice of force field manoj singh (Sun May 31 2009 - 13:39:13 PDT)
- Last message date: Mon Jun 01 2009 - 01:11:52 PDT
- Archived on: Fri Dec 27 2024 - 05:53:49 PST
