Amber Archive Feb 2013 by thread
- [AMBER] scaling problem in RADIAL of CPPTRAJ Marek Maly (Thu Jan 31 2013 - 15:47:13 PST)
- [AMBER] AMBER 10 install issue Joel Tyndall (Thu Jan 31 2013 - 17:27:50 PST)
- [AMBER] Problem using solvatebox for large, linear peptide Joe Passman (Thu Jan 31 2013 - 18:16:09 PST)
- [AMBER] Can we model the solvent implicitly outside a solvent shell (irregular shape) Debayan Chakraborty (Thu Jan 31 2013 - 19:29:49 PST)
- Re: [AMBER] Fwd: Regarding the problem with ligand conformation aneesh cna (Fri Feb 01 2013 - 01:05:58 PST)
- Re: [AMBER] How to save secondary structure gnuplot as image HM (Fri Feb 01 2013 - 07:06:58 PST)
- [AMBER] Query regarding cpptraj multiple input in a single file HM (Fri Feb 01 2013 - 07:11:59 PST)
- Re: [AMBER] error while running mmpbsa.py in amber12 Ismail, Mohd F. (Fri Feb 01 2013 - 14:22:19 PST)
- [AMBER] Fwd: Sampling of a point by a molecule while keeping the relative position of the molecule unchanged in TMD Sajeewa Pemasinghe (Fri Feb 01 2013 - 14:59:54 PST)
- [AMBER] protein-protein binding free energy Date, Mihir (Fri Feb 01 2013 - 15:14:33 PST)
- [AMBER] Error initiating H-REMD Brian Radak (Fri Feb 01 2013 - 15:52:32 PST)
- [AMBER] A doubt about averaging time in dynamic cross-correlation analysis aneesh cna (Sat Feb 02 2013 - 02:17:42 PST)
- [AMBER] Problems with ti using DFTB for zinc bound hydroxyl Fabrício Bracht (Sat Feb 02 2013 - 11:35:04 PST)
- [AMBER] Setting up a Periodic Box Size Jonathan Saboury (Sat Feb 02 2013 - 11:36:15 PST)
- Re: [AMBER] about iwrap=1 and ntxo=2 Thomas Evangelidis (Sat Feb 02 2013 - 12:08:40 PST)
- [AMBER] igb=7 & 8 CalcError: "pathway" failed with prmtop "protein".prmtop psu4.uic.edu (Sat Feb 02 2013 - 15:48:00 PST)
- [AMBER] ERROR: the best APS is not zero, bonds involved by this atom are frozen Jonathan Saboury (Sun Feb 03 2013 - 20:44:08 PST)
- [AMBER] amber11 installation test files Mary Varughese (Sun Feb 03 2013 - 21:11:30 PST)
- [AMBER] density calculation in radial cpptraj Asmita Gupta (Mon Feb 04 2013 - 02:08:24 PST)
- [AMBER] espgen cannot deal with Gaussian 09 log file HIMANSHU JOSHI (Mon Feb 04 2013 - 03:51:52 PST)
- Re: [AMBER] AMBER pmemd and pmemd.cuda, not restart files after minimization - fort.16 file instead Marko Wehle (Mon Feb 04 2013 - 04:31:21 PST)
- [AMBER] use of parmbsc0 for protein-DNA complex along with ff99SB Sangita Kachhap (Mon Feb 04 2013 - 04:39:14 PST)
- [AMBER] silhouette.pl Tamer Ibrahim (Mon Feb 04 2013 - 07:35:45 PST)
- [AMBER] AMBER-Tools cpptraj residue numbering incorrect Marko Wehle (Mon Feb 04 2013 - 07:52:55 PST)
- [AMBER] phosporylated residue connectivity problem BALA SUBRAMANI G L (Tue Feb 05 2013 - 01:15:14 PST)
- [AMBER] Hbond analysis in ptraj DEBOSTUTI GHOSHDASTIDAR (Tue Feb 05 2013 - 05:07:17 PST)
- [AMBER] active site rmsd (residue 5A around bound ligand) ??? HM (Tue Feb 05 2013 - 05:40:45 PST)
- [AMBER] iAPBS George Tzotzos (Tue Feb 05 2013 - 05:57:31 PST)
- Re: [AMBER] (no subject) BERGY (Tue Feb 05 2013 - 07:05:31 PST)
- [AMBER] Fwd: BERGY (Tue Feb 05 2013 - 07:07:04 PST)
- [AMBER] rmsd of Ethanol Chinthaka Ratnaweera (Tue Feb 05 2013 - 08:37:37 PST)
- [AMBER] Could you please remove me from AMBER mailing list Yulin Huang (Tue Feb 05 2013 - 09:32:48 PST)
- [AMBER] 3D-RISM input file error WenJuan Huang (Tue Feb 05 2013 - 11:05:43 PST)
- [AMBER] OPLS to AMBER vdw parameters conversion Prabal Maiti (Tue Feb 05 2013 - 12:07:01 PST)
- [AMBER] setting certain atoms as static Jonathan Saboury (Tue Feb 05 2013 - 23:14:11 PST)
- [AMBER] Query about checking of convergence in REMD gargi borgohai (Wed Feb 06 2013 - 04:21:24 PST)
- [AMBER] charge for NMA molecule Subrata Paul (Wed Feb 06 2013 - 04:58:57 PST)
- [AMBER] hbond analysis acceptor atoms DEBOSTUTI GHOSHDASTIDAR (Wed Feb 06 2013 - 09:08:50 PST)
- [AMBER] ptraj RMSD- spikes in RMSD and co-ordinates at 0.000 Cassandra Churchill (Wed Feb 06 2013 - 09:58:18 PST)
- [AMBER] problems with NAB uday spike (Wed Feb 06 2013 - 23:49:37 PST)
- [AMBER] Adding buffer and salt Indrajit Deb (Thu Feb 07 2013 - 00:23:55 PST)
- [AMBER] simulation MD - basic questions Anne Kichler (Thu Feb 07 2013 - 02:54:17 PST)
- [AMBER] issues with PDB file and tleap Massimiliano Porrini (Thu Feb 07 2013 - 03:45:58 PST)
- [AMBER] parmed.py error IndexError: list index out of range Jio M (Thu Feb 07 2013 - 07:52:49 PST)
- [AMBER] problem with strip water some distance away from peptide Do Yong Kim (Thu Feb 07 2013 - 16:03:16 PST)
- [AMBER] missing parameter of B in .frcmod 纪晓峰 (Thu Feb 07 2013 - 19:19:54 PST)
- [AMBER] restart file with *********** problem Dr. M. Venkata Satish Kumar (Fri Feb 08 2013 - 00:18:19 PST)
- [AMBER] change starting time of simulation Thomas Evangelidis (Fri Feb 08 2013 - 01:38:19 PST)
- [AMBER] NMA(n-methylacetamide) Subrata Paul (Fri Feb 08 2013 - 02:12:31 PST)
- [AMBER] NaN error in restart file Shobana, G . (Fri Feb 08 2013 - 02:26:46 PST)
- [AMBER] Problem related with umbrella sampling Sindrila Dutta banik (Fri Feb 08 2013 - 03:20:13 PST)
- [AMBER] problem with 3-ring system in antechamber Leandro Bortot (Fri Feb 08 2013 - 07:59:49 PST)
- [AMBER] Problem related to the umbrella sampling Sindrila Dutta banik (Fri Feb 08 2013 - 09:30:03 PST)
- [AMBER] problem with umbrella sampling Sindrila Dutta banik (Fri Feb 08 2013 - 09:33:13 PST)
- [AMBER] Problem in running TREMD in AMBER10 Sajeewa Pemasinghe (Fri Feb 08 2013 - 12:37:45 PST)
- [AMBER] Amber 12 and CUDA 5.0 K20 vs GTX 680: GTX 680 is two time faster than K20 Filippo Pullara (Fri Feb 08 2013 - 13:05:21 PST)
- [AMBER] PMEMD amd mmpbsa.py mpi Chris Chris (Fri Feb 08 2013 - 16:08:44 PST)
- [AMBER] problem using autoimage from cpptraj Jonathan Saboury (Fri Feb 08 2013 - 20:35:23 PST)
- [AMBER] Query regarding PNA-DNA duplex parameterization in AMBER Souvik Sur (Fri Feb 08 2013 - 23:26:19 PST)
- [AMBER] xleap could not find the type Cl- Sanjib Paul (Sat Feb 09 2013 - 04:26:32 PST)
- Re: [AMBER] distance restraints between the primary molecule and its periodic image Scott Le Grand (Sat Feb 09 2013 - 10:17:30 PST)
- [AMBER] Problems with MMPBSA.py for running pbsa calculations manikanthan bhavaraju (Sat Feb 09 2013 - 12:36:19 PST)
- [AMBER] Issues with idecomp Adam Mepham (Sat Feb 09 2013 - 20:55:19 PST)
- [AMBER] Wrong Annotation of PREPIN generated by RESIDUEGEN kurisaki (Sun Feb 10 2013 - 01:20:26 PST)
- [AMBER] Using cpptraj to trim a range of water residues while maintaining a periodic box Joe Passman (Sun Feb 10 2013 - 17:15:21 PST)
- [AMBER] Inquiry from beginner rajith bhaskar (Sun Feb 10 2013 - 20:55:15 PST)
- [AMBER] Application of mmpbsa DEBOSTUTI GHOSHDASTIDAR (Sun Feb 10 2013 - 21:46:31 PST)
- [AMBER] Warnings when saving prmtop and inpcrd files. Sanjib Paul (Sun Feb 10 2013 - 23:39:51 PST)
- [AMBER] Hydrogens AMBER 1H6 and 2H6 vs. Glycam H61 and H62 for Glucose Kepa K. Burusco (Mon Feb 11 2013 - 05:48:07 PST)
- [AMBER] Error running large number of trajectories with multisander Brian Radak (Mon Feb 11 2013 - 07:42:21 PST)
- [AMBER] PSF file, atom radii and chamber Massimiliano Porrini (Mon Feb 11 2013 - 10:05:48 PST)
- [AMBER] Issues with idecomp Adam Mepham (Mon Feb 11 2013 - 14:17:30 PST)
- [AMBER] Compilation problems for parallel build after applying patches Miguel Ortiz Lombardía (Tue Feb 12 2013 - 06:55:18 PST)
- [AMBER] A general question about umbrella sampling Sajeewa Pemasinghe (Tue Feb 12 2013 - 12:51:47 PST)
- Re: [AMBER] Building a new structure! Ibrahim Said (Wed Feb 13 2013 - 00:37:50 PST)
- [AMBER] Anomalous Termination of PMEMD.CUDA jobs kurisaki (Wed Feb 13 2013 - 02:02:23 PST)
- [AMBER] VIBRATIONAL FREQUANCY USING NMODE Rasha Alqus (Wed Feb 13 2013 - 05:32:43 PST)
- [AMBER] MMPBSA.py: about sasopt value with inp=1 Miguel Ortiz Lombardía (Wed Feb 13 2013 - 05:55:45 PST)
- [AMBER] Cannot open the input file: XYZ.pdb in rpdb(), exit Matthias Leeder (Wed Feb 13 2013 - 10:42:02 PST)
- [AMBER] charged molecule with antechamber Rebeca García Fandiño (Wed Feb 13 2013 - 10:45:47 PST)
- [AMBER] simulation of a nucleic acid linked on a gold surface Barbault Florent (Wed Feb 13 2013 - 11:54:18 PST)
- [AMBER] idecomp output frequency Adam Mepham (Wed Feb 13 2013 - 17:56:20 PST)
- [AMBER] problems starting amber Ayesha Fatima (Wed Feb 13 2013 - 19:00:02 PST)
- [AMBER] What algorithm does ptraj use for solvation of eigen-value problem. kurisaki (Fri Feb 15 2013 - 01:08:46 PST)
- [AMBER] test David A Case (Fri Feb 15 2013 - 08:13:33 PST)
- [AMBER] Sander error - Segmentation fault (core dumped) Symon Gathiaka (Fri Feb 15 2013 - 11:28:51 PST)
- [AMBER] Small bug in MMPBSA.py tutorial George A. Khoury (Sat Feb 16 2013 - 09:47:03 PST)
- [AMBER] MM PBSA and entropy decomposition Aron Broom (Sat Feb 16 2013 - 10:06:30 PST)
- [AMBER] pka calculation energy by residue Adam Mepham (Sat Feb 16 2013 - 15:46:28 PST)
- [AMBER] the position of counterion Sun (Sun Feb 17 2013 - 10:54:00 PST)
- [AMBER] atomic pair correlation function through PCA Date, Mihir (Sun Feb 17 2013 - 20:35:26 PST)
- [AMBER] PCA analysis query Vaibhav Dixit (Sun Feb 17 2013 - 23:34:23 PST)
- [AMBER] Error with MMPBSA calculation aneesh cna (Mon Feb 18 2013 - 01:21:56 PST)
- [AMBER] xleap problem using savemol2 Charles Do (Mon Feb 18 2013 - 10:44:38 PST)
- [AMBER] Defining parameters for and undefined element. Solid Surface gabrielg.uvic.ca (Mon Feb 18 2013 - 14:10:14 PST)
- [AMBER] PROBLEMS IN SETTING UP PHOSPHORYLATED SIMULATION MODELS Theodosia Teo (Mon Feb 18 2013 - 19:46:53 PST)
- [AMBER] Analysis in ptraj gargi borgohai (Tue Feb 19 2013 - 01:38:29 PST)
- [AMBER] Dumping of center of mass coordinates of protein domain HM (Tue Feb 19 2013 - 04:11:18 PST)
- [AMBER] problem in running MMPBSA Saugata Hazra (Tue Feb 19 2013 - 05:02:45 PST)
- [AMBER] Missing comma in input file Sasha Perkins (Tue Feb 19 2013 - 08:18:03 PST)
- [AMBER] How to calculate the vibrational frequancy Rasha Alqus (Tue Feb 19 2013 - 08:47:11 PST)
- [AMBER] problem reading CHARMM lipid parameters into chamber Sally Pias (Tue Feb 19 2013 - 13:07:56 PST)
- [AMBER] qmshake=1 did not prevent bonds from being broken Fabrício Bracht (Tue Feb 19 2013 - 14:32:49 PST)
- [AMBER] Kepler GTX680 MD Workstation Charles Do (Tue Feb 19 2013 - 19:12:31 PST)
- [AMBER] Problem related to different version of amber Changqing Yan (Tue Feb 19 2013 - 23:42:18 PST)
- Re: [AMBER] short bonds in average pdb Vaibhav Dixit (Wed Feb 20 2013 - 01:04:37 PST)
- [AMBER] randomizeions with cpptraj Asmita Gupta (Wed Feb 20 2013 - 02:56:43 PST)
- [AMBER] problem in nmode Rasha Alqus (Wed Feb 20 2013 - 06:39:39 PST)
- [AMBER] mmpbsa_py_nabnmode for single macromolecule Rasha Alqus (Wed Feb 20 2013 - 07:27:16 PST)
- [AMBER] glucose marta wisniewska. (Wed Feb 20 2013 - 07:58:25 PST)
- [AMBER] ODP: Re: glucose m.wisniewska.aol.pl (Wed Feb 20 2013 - 09:11:09 PST)
- [AMBER] Problem with xleap/tleap Ibrahim Moustafa (Wed Feb 20 2013 - 10:14:07 PST)
- [AMBER] About EPTOT Mo Chen (Wed Feb 20 2013 - 15:50:01 PST)
- [AMBER] Amber 11 Installment problem Changqing Yan (Wed Feb 20 2013 - 19:14:31 PST)
- [AMBER] Using OPLS force field parameters in Amber MD run DEBOSTUTI GHOSHDASTIDAR (Wed Feb 20 2013 - 23:13:56 PST)
- [AMBER] radial distribution function between atoms of the two masks Massimiliano Porrini (Thu Feb 21 2013 - 06:12:24 PST)
- [AMBER] crgmask and qmmm region compatibility Fabrício Bracht (Thu Feb 21 2013 - 06:44:02 PST)
- [AMBER] constant pH for transmemrane proteins Thomas Evangelidis (Thu Feb 21 2013 - 07:19:13 PST)
- [AMBER] leap insert missing atoms in aminoacids according to ... Marta Perez (Thu Feb 21 2013 - 07:59:20 PST)
- [AMBER] Linear peptide using non standard amino acids moitrayee.mbu.iisc.ernet.in (Thu Feb 21 2013 - 13:12:03 PST)
- [AMBER] amber error about protein containing heme tianchuan1015 (Thu Feb 21 2013 - 23:58:31 PST)
- [AMBER] regarding frcmod preparation Aparna P (Fri Feb 22 2013 - 03:07:46 PST)
- [AMBER] ligand moving out of protein incorrect imaging of trajectory using image and center commands with amber 10 ET (Fri Feb 22 2013 - 10:10:20 PST)
- [AMBER] unspecified launch failure launching kernel kRecalculateVelocities Symon Gathiaka (Fri Feb 22 2013 - 10:58:04 PST)
- [AMBER] Calculating Hydrogen bond energy Ahmed Ayoub (Fri Feb 22 2013 - 23:55:01 PST)
- [AMBER] possibility to increase max . num. of bonded atoms ? Marek Maly (Sat Feb 23 2013 - 19:43:18 PST)
- [AMBER] spectrum simulation francesco oteri (Sun Feb 24 2013 - 12:56:18 PST)
- [AMBER] dihedral distribution plot colvin (Sun Feb 24 2013 - 21:33:06 PST)
- [AMBER] Fwd: Installing Amber in parallel whit Lion javier alejandro rendon carrillo (Sun Feb 24 2013 - 22:17:12 PST)
- [AMBER] PBSA vs MMPBSA.py eneas.usal.es (Sun Feb 24 2013 - 23:57:12 PST)
- [AMBER] pseudoatom Anne Kichler (Mon Feb 25 2013 - 03:32:41 PST)
- [AMBER] amber phosphorylated parameters Neha Gandhi (Mon Feb 25 2013 - 04:01:07 PST)
- [AMBER] Error in RNA simulation esmaeel azadian (Mon Feb 25 2013 - 04:25:14 PST)
- [AMBER] mmgbsa minimisation failing with error in trajene() ET (Mon Feb 25 2013 - 04:42:14 PST)
- [AMBER] heme parameters Giulia (Mon Feb 25 2013 - 05:58:15 PST)
- [AMBER] amber 11 installation on server Mary Varughese (Mon Feb 25 2013 - 10:24:31 PST)
- [AMBER] Question regarding wham and umbrella sampling Fabrício Bracht (Mon Feb 25 2013 - 12:09:23 PST)
- [AMBER] converting AMBER minimized file to PDB/MOL2 Shashidhar Rao (Mon Feb 25 2013 - 12:17:26 PST)
- [AMBER] question on input for MMPBSA.py Shashidhar Rao (Mon Feb 25 2013 - 13:08:32 PST)
- [AMBER] MMPBSA problem Tommy Yap (Mon Feb 25 2013 - 18:15:05 PST)
- [AMBER] Problem related to the bfactor calculation Sindrila Dutta banik (Mon Feb 25 2013 - 21:03:39 PST)
- [AMBER] force field file 徐立平 (Mon Feb 25 2013 - 23:53:29 PST)
- [AMBER] MMPBSA free energy Soumya Lipsa Rath (Tue Feb 26 2013 - 03:50:13 PST)
- [AMBER] adding rings using sequence command Jio M (Tue Feb 26 2013 - 06:55:50 PST)
- [AMBER] error in nmode Rasha Alqus (Tue Feb 26 2013 - 08:46:16 PST)
- [AMBER] bond angle fitting CHAMI F. (Tue Feb 26 2013 - 11:17:09 PST)
- [AMBER] TI without ifsc = 1 crashes Fabrício Bracht (Tue Feb 26 2013 - 15:02:32 PST)
- [AMBER] NPT with pmemd.amoeba.MPI Density alway decreasing Cheng Wang (Tue Feb 26 2013 - 15:30:56 PST)
- [AMBER] Install amber in Mac Lion javier alejandro rendon carrillo (Tue Feb 26 2013 - 16:57:16 PST)
- [AMBER] periodic image of octahedron box in VMD 吴云剑 (Tue Feb 26 2013 - 18:10:08 PST)
- [AMBER] error in nmode Rasha Alqus (Wed Feb 27 2013 - 07:03:03 PST)
- [AMBER] Error analysing an RNA trajectory with anal Amparo Garcia Lopez (Wed Feb 27 2013 - 10:44:50 PST)
- [AMBER] MMGBSA/MMPBSA Decomposition Analysis Vivek Shankar Bharadwaj (Wed Feb 27 2013 - 16:28:38 PST)
- Re: [AMBER] 0 meandme_meandme2003.yahoo.com (Wed Feb 27 2013 - 19:54:29 PST)
- [AMBER] remd exchange acceptance Kim Hyunsik (Wed Feb 27 2013 - 22:08:24 PST)
- [AMBER] GTX 680 vs GTX Titan Gonzalo Jimenez (Wed Feb 27 2013 - 23:22:33 PST)
- [AMBER] generate MDCRD file for two points HM (Thu Feb 28 2013 - 04:00:32 PST)
- [AMBER] aMD Beale, John (Thu Feb 28 2013 - 05:27:17 PST)
- Re: [AMBER] Problem to run sander with more than 60 atom types Elise Duboué-Dijon (Thu Feb 28 2013 - 06:24:10 PST)
- Re: [AMBER] Modified amino acid parameter generation moitrayee.mbu.iisc.ernet.in (Thu Feb 28 2013 - 09:59:28 PST)
- [AMBER] Amber MD using NAMD Ilyas Yildirim (Thu Feb 28 2013 - 15:32:32 PST)
- [AMBER] PCI-E 2.0 vs 3.0 (AMD vs INTEL?) Jonathan Gough (Thu Feb 28 2013 - 18:53:41 PST)
- Last message date: Thu Feb 28 2013 - 19:00:03 PST
- Archived on: Fri Nov 22 2024 - 05:54:40 PST
