Amber Archive Feb 2011 by thread
- Re: [AMBER] sander on amber12 setyanto md (Mon Jan 31 2011 - 18:58:42 PST)
- Re: [AMBER] REMD equilibration restart Sangita Kachhap (Mon Jan 31 2011 - 19:28:21 PST)
- [AMBER] 回复： 回复： 回复： 回复： MM-PBSA error about protein + Mg2+ 475649770 (Mon Jan 31 2011 - 22:29:30 PST)
- [AMBER] MMPBSA printres syntax Jesper Sørensen (Tue Feb 01 2011 - 01:30:29 PST)
- [AMBER] TI in vacuum FCUP (Tue Feb 01 2011 - 06:36:55 PST)
- [AMBER] frcmod.urea subrata paul (Tue Feb 01 2011 - 07:07:49 PST)
- [AMBER] Amber11 parallel testing error Zhu, James (Tue Feb 01 2011 - 08:36:18 PST)
- [AMBER] Regarding NVIDIA Graphics Card Hirdesh Kumar (Tue Feb 01 2011 - 09:05:19 PST)
- [AMBER] PMF problem dhacademic (Tue Feb 01 2011 - 12:55:30 PST)
- [AMBER] Create EtOHbox Mattei, Alessandra (Tue Feb 01 2011 - 14:43:45 PST)
- Re: [AMBER] installing ambertools1.4 Vijay Manickam Achari (Tue Feb 01 2011 - 23:57:43 PST)
- [AMBER] Energy calculation with namdenergy and amber Jakob Luchner (Wed Feb 02 2011 - 09:15:46 PST)
- [AMBER] Amber11 parallel configure error Zhu, James (Wed Feb 02 2011 - 09:53:10 PST)
- [AMBER] Can anyone suggest me solution vani panguluri (Wed Feb 02 2011 - 11:33:16 PST)
- [AMBER] pol3 water droplet Yubo Fan (Wed Feb 02 2011 - 12:33:22 PST)
- [AMBER] clustering by attribute Massimiliano Porrini (Wed Feb 02 2011 - 15:20:22 PST)
- [AMBER] Dielectric constant for solute mish (Thu Feb 03 2011 - 06:31:22 PST)
- [AMBER] pol3 water droplet Yubo Fan (Thu Feb 03 2011 - 13:11:30 PST)
- [AMBER] Membrane Protein Simulation Hirdesh Kumar (Thu Feb 03 2011 - 20:44:25 PST)
- Re: [AMBER] free radicals in amber Ashutosh Shandilya (Fri Feb 04 2011 - 06:09:03 PST)
- [AMBER] REMD production run restart Sangita Kachhap (Fri Feb 04 2011 - 07:21:28 PST)
- [AMBER] MOIL-view alternatives Emanuele G (Fri Feb 04 2011 - 08:29:07 PST)
- [AMBER] 3 GB GTX580s Scott Le Grand (Fri Feb 04 2011 - 14:29:33 PST)
- [AMBER] MM-PBSA error Jagur Lambix (Fri Feb 04 2011 - 15:39:09 PST)
- [AMBER] measruement of effect of perticular water molecule on affinity and specificity Sangita Kachhap (Fri Feb 04 2011 - 23:13:31 PST)
- [AMBER] pdb error subrata paul (Sat Feb 05 2011 - 21:27:09 PST)
- Re: [AMBER] ptraj (AT 1.4) hiccups with gzipped trajectory files Kamali Sripathi (Sun Feb 06 2011 - 09:51:22 PST)
- [AMBER] Kindly help me out for the following errors during installation of AmberTools amit banerjee (Sun Feb 06 2011 - 22:11:56 PST)
- [AMBER] AMBER11 MMPBSA.py tutorial section 3.6 Yokota_Akihiro.takeda.co.jp (Sun Feb 06 2011 - 23:54:11 PST)
- [AMBER] ncsu-umbrella-slice utility in AMBER11 Mark Santer (Mon Feb 07 2011 - 04:07:15 PST)
- [AMBER] Distance restraints Beale, John (Mon Feb 07 2011 - 09:59:35 PST)
- [AMBER] softcore TI with more than 2 procs? Niel Henriksen (Mon Feb 07 2011 - 10:40:26 PST)
- [AMBER] Structural alignment & RMSD calculation Rahul Banerjee (Mon Feb 07 2011 - 10:50:14 PST)
- [AMBER] Ionic strength in MM-PBSA Robert Elder (Mon Feb 07 2011 - 13:14:28 PST)
- [AMBER] AmberTools 1.4 parallel programs Martin M. Ossowski (Mon Feb 07 2011 - 13:44:13 PST)
- [AMBER] XMIN ERROR in LMOD calculation Wong, Sergio E. (Mon Feb 07 2011 - 16:34:18 PST)
- [AMBER] Ptraj Translate Error Hirdesh Kumar (Mon Feb 07 2011 - 21:02:58 PST)
- [AMBER] New to Amber Ashok Das Mahapatra (Tue Feb 08 2011 - 04:00:42 PST)
- [AMBER] compilation failure of amber 11 on Itanium2 Yubo Fan (Tue Feb 08 2011 - 12:18:48 PST)
- [AMBER] pmemd.cuda issues on Tesla S2050 Sasha Buzko (Tue Feb 08 2011 - 16:57:37 PST)
- [AMBER] How to rename GLYCAM residue names of a sugar to the same name for one complete sugar (in tleap or xleap) mish (Wed Feb 09 2011 - 07:30:02 PST)
- [AMBER] break down of simulation after approximately 60 ns Jakob Luchner (Wed Feb 09 2011 - 11:36:25 PST)
- [AMBER] problems with mm_pbsa on amber8 Waqas Nasir (Thu Feb 10 2011 - 04:22:59 PST)
- [AMBER] parametrization of sugar modified nucleic acids Aparna P (Fri Feb 11 2011 - 01:46:13 PST)
- Re: [AMBER] parametrization of sugar modified nucleic acids Stephane Abel (Fri Feb 11 2011 - 05:43:05 PST)
- Re: [AMBER] parametrization of sugar modified nucleic acids cieplak.cgl.ucsf.edu (Fri Feb 11 2011 - 11:25:19 PST)
- Re: [AMBER] parametrization of sugar modified nucleic acids Aparna P (Sun Feb 13 2011 - 22:31:37 PST)
- [AMBER] AMBER 9 install gfortran gromacs (Sun Feb 13 2011 - 23:15:07 PST)
- Re: [AMBER] AMBER 9 install gfortran Jason Swails (Mon Feb 14 2011 - 04:41:27 PST)
- [AMBER] AMBER 9 install gfortran, not need AmberTool gromacs (Mon Feb 14 2011 - 16:20:24 PST)
- Re: [AMBER] AMBER 9 install gfortran, not need AmberTool Jason Swails (Mon Feb 14 2011 - 16:42:54 PST)
- Re: [AMBER] AMBER 9 install gfortran, not need AmberTool gromacs (Mon Feb 14 2011 - 17:04:24 PST)
- Re: [AMBER] AMBER 9 install gfortran, not need AmberTool Jason Swails (Mon Feb 14 2011 - 17:47:39 PST)
- Re: [AMBER] AMBER 9 install gfortran, not need AmberTool gromacs (Mon Feb 14 2011 - 17:20:11 PST)
- Re: [AMBER] AMBER 9 install gfortran, not need AmberTool Jason Swails (Mon Feb 14 2011 - 17:48:59 PST)
- Re: [AMBER] AMBER 9 install gfortran, not need AmberTool gromacs (Mon Feb 14 2011 - 17:41:16 PST)
- Re: [AMBER] AMBER 9 install gfortran, not need AmberTool Jason Swails (Mon Feb 14 2011 - 17:53:13 PST)
- Re: [AMBER] AMBER 9 install gfortran, not need AmberTool gromacs (Mon Feb 14 2011 - 18:47:17 PST)
- Re: [AMBER] AMBER 9 install gfortran, not need AmberTool David Case (Mon Feb 14 2011 - 19:17:46 PST)
- Re: [AMBER] AMBER 9 install gfortran, not need AmberTool gromacs (Mon Feb 14 2011 - 19:27:00 PST)
- Re: [AMBER] AMBER 9 install gfortran, not need AmberTool case (Tue Feb 15 2011 - 04:45:15 PST)
- [AMBER] AMBER 9 install gfortran, If i install xorg-dev package, there will be error; However if i did not install xorg-dev, i cannot pass the test of tleap. gromacs (Mon Feb 14 2011 - 19:17:39 PST)
- Re: [AMBER] AMBER 9 install gfortran, If i install xorg-dev package, there will be error; However if i did not install xorg-dev, i cannot pass the test of tleap. Jason Swails (Mon Feb 14 2011 - 19:40:05 PST)
- Re: [AMBER] AMBER 9 install gfortran case (Mon Feb 14 2011 - 05:04:40 PST)
- [AMBER] Consistency between temperatures in mdout and mdcrd in REMD Daniel Sindhikara (Fri Feb 11 2011 - 02:08:05 PST)
- [AMBER] MMPBSA.py - dimer energy calculations Julia Romanowska (Fri Feb 11 2011 - 03:34:02 PST)
- [AMBER] Polymeric lattice building tommaso.casalini.mail.polimi.it (Fri Feb 11 2011 - 03:45:18 PST)
- [AMBER] ERROR IN SETPAR() when REMD running Bongkeun Kim (Fri Feb 11 2011 - 09:25:40 PST)
- [AMBER] Cluster considerations peker milas (Fri Feb 11 2011 - 16:33:39 PST)
- [AMBER] create urea molecule. subrata paul (Fri Feb 11 2011 - 23:22:54 PST)
- [AMBER] problem with analyzing trajectaries bharat lakhani (Sat Feb 12 2011 - 00:41:32 PST)
- [AMBER] parametrization of acetyl-coa using antechamber Knut Jørgen Bjuland (Sat Feb 12 2011 - 10:29:24 PST)
- [AMBER] EVB with time-dependent coupling parameter? Jose Borreguero (Sat Feb 12 2011 - 11:15:59 PST)
- [AMBER] slowly relaxing individual residues Andre Serobian (Sun Feb 13 2011 - 12:07:21 PST)
- [AMBER] Two fragments minimization Eliac Brown (Sun Feb 13 2011 - 13:23:00 PST)
- [AMBER] ISTRNG in PBSA script does not work properly Xioling Chuang (Sun Feb 13 2011 - 23:24:05 PST)
- [AMBER] Problem with QMMM umbrella sampling Wook Lee (Mon Feb 14 2011 - 02:06:19 PST)
- [AMBER] new force field ff99SBildn not supported for normal mode analysis in amber11 Tan Yaw Sing (Mon Feb 14 2011 - 10:23:29 PST)
- [AMBER] Regarding AMBER help command and Ewald Namelist Variables Specifications Naveen Samala (Mon Feb 14 2011 - 11:06:34 PST)
- [AMBER] max pairlist cutoff error on octahedral box Bongkeun Kim (Mon Feb 14 2011 - 11:11:50 PST)
- [AMBER] ESURF term error in a one-step sander calculation Yao-Chi Chen (Mon Feb 14 2011 - 18:00:44 PST)
- [AMBER] parameters for CO2+ moitrayee.mbu.iisc.ernet.in (Mon Feb 14 2011 - 22:05:31 PST)
- [AMBER] Simulation of DNA using generalized Born model Ali M. Naserian-Nik (Tue Feb 15 2011 - 00:15:46 PST)
- [AMBER] TI problem - Antechamber changes the atom order FCUP (Tue Feb 15 2011 - 03:27:31 PST)
- [AMBER] increasing rmsd value Siti Mohamad (Tue Feb 15 2011 - 05:07:04 PST)
- [AMBER] 回复： 回复： 回复： 回复： 回复： MM-PBSA error about protein + Mg2+ 475649770 (Tue Feb 15 2011 - 05:05:31 PST)
- [AMBER] REMD at constant pH Cheng-I Lee (Tue Feb 15 2011 - 05:30:26 PST)
- [AMBER] Fwd: ESURF term error in a one-step sander calculation Yao-Chi Chen (Tue Feb 15 2011 - 10:10:31 PST)
- [AMBER] 回复： 回复： 回复： 回复： 回复： MM-PBSA error about protein + Mg2+ 475649770 (Tue Feb 15 2011 - 05:07:49 PST)
- [AMBER] xleap does not want to impose my dihedrals steinbrt.rci.rutgers.edu (Tue Feb 15 2011 - 10:27:27 PST)
- [AMBER] xleap or rather ff10 bug? update steinbrt.rci.rutgers.edu (Tue Feb 15 2011 - 10:47:25 PST)
- [AMBER] FATAL ERROR vani panguluri (Tue Feb 15 2011 - 16:02:09 PST)
- [AMBER] 回复： 回复： 回复： 回复： 回复： 回复： MM-PBSA error about protein + Mg2+ 475649770 (Tue Feb 15 2011 - 16:56:59 PST)
- [AMBER] ERROR IN SETPAR() upon atom distribution with FF03, 03.r1 Bongkeun Kim (Tue Feb 15 2011 - 17:19:56 PST)
- [AMBER] 回复： 回复： 回复： 回复： 回复： 回复： 回复： MM-PBSA error about protein + Mg2+ 475649770 (Wed Feb 16 2011 - 00:45:15 PST)
- [AMBER] cluster using ptraj 475649770 (Wed Feb 16 2011 - 01:29:20 PST)
- [AMBER] MD of protein with NADPH Aditya Padhi (Wed Feb 16 2011 - 01:50:48 PST)
- [AMBER] 回复： 回复： 回复： 回复： 回复： 回复： 回复： 回复： MM-PBSA error about protein + Mg2+ 475649770 (Wed Feb 16 2011 - 04:42:27 PST)
- [AMBER] Fwd: About long simulation haris p (Wed Feb 16 2011 - 07:47:19 PST)
- [AMBER] V5 dihedrals serena_leone.libero.it (Wed Feb 16 2011 - 08:21:50 PST)
- [AMBER] restraining protons with pmemd Francesco Pietra (Wed Feb 16 2011 - 10:11:50 PST)
- [AMBER] R: Re: V5 dihedrals serena_leone.libero.it (Wed Feb 16 2011 - 10:29:00 PST)
- [AMBER] AMBER Workshop in Barcelona, Spain, May 3rd to 6th 2011. Ross Walker (Wed Feb 16 2011 - 12:16:01 PST)
- [AMBER] Simple NAB script from manual segfaults at call to md() Chris King (Wed Feb 16 2011 - 14:35:26 PST)
- [AMBER] Query regarding atom type using xleap Hirdesh Kumar (Wed Feb 16 2011 - 22:37:28 PST)
- [AMBER] setBox command in sleap AMBER11 Antje Wolf (Thu Feb 17 2011 - 04:02:52 PST)
- [AMBER] center of mass motion siddesh southekal (Thu Feb 17 2011 - 05:09:28 PST)
- [AMBER] binding energy calculation problem poll.chemie.uni-hamburg.de (Thu Feb 17 2011 - 07:13:25 PST)
- [AMBER] problem with parametrization of an organo-metallic cluster using RED server moitrayee.mbu.iisc.ernet.in (Thu Feb 17 2011 - 00:18:13 PST)
- [AMBER] Scale sander.MPI to 64 ncpus - Amber11 Leong Wye Kit Damien (Thu Feb 17 2011 - 09:05:09 PST)
- [AMBER] MD simulation of protein with Calcium ion Aditya Padhi (Thu Feb 17 2011 - 21:31:28 PST)
- [AMBER] How to simulate hydration free energy with thermodynamic integration? Junjian Miao (Fri Feb 18 2011 - 05:32:18 PST)
- [AMBER] How to simulate hydration free energy with thermodynamic integration? Junjian Miao (Fri Feb 18 2011 - 05:45:49 PST)
- [AMBER] Probelm with antechamber for resp charge derivation Rajesh Raju (Fri Feb 18 2011 - 09:52:50 PST)
- [AMBER] Extracting replica trajectories Cheng-I Lee (Sun Feb 20 2011 - 01:11:04 PST)
- [AMBER] Angle setting tommaso.casalini.mail.polimi.it (Sun Feb 20 2011 - 06:37:30 PST)
- [AMBER] reimaging failure Francesco Pietra (Sun Feb 20 2011 - 09:29:53 PST)
- [AMBER] How to generate MM/PBSA statistics from recovered Job mish (Mon Feb 21 2011 - 07:38:24 PST)
- [AMBER] PTRAJ and segmentation faults Seibold, Stephen (Mon Feb 21 2011 - 12:56:03 PST)
- [AMBER] MM-PBSA: PB bomb in pb_reslist(): maxnbr too small manikanthan bhavaraju (Mon Feb 21 2011 - 18:02:22 PST)
- [AMBER] restraints in Targeted Molecular dynamics siddesh southekal (Tue Feb 22 2011 - 02:20:52 PST)
- [AMBER] Problems with mmpbsa moacyr comar (Tue Feb 22 2011 - 05:15:23 PST)
- [AMBER] Use of semiempirical QM/MM method in Amber to obtain free energy profile of a reaction Dmitry Nilov (Tue Feb 22 2011 - 08:11:29 PST)
- [AMBER] Energy Calculation Problem Nitu Bansal (Tue Feb 22 2011 - 08:33:07 PST)
- [AMBER] Fwd: [ics.uci.edu #33898] Fwd: Amber11 download instructions Lane Votapka (Tue Feb 22 2011 - 09:30:40 PST)
- [AMBER] developing parameters for Zn-binding site Jorgen Simonsen (Tue Feb 22 2011 - 09:44:10 PST)
- [AMBER] Gasteiger parameter Eliac Brown (Tue Feb 22 2011 - 16:45:57 PST)
- [AMBER] how to simulate solute in vacuum with TI Junjian Miao (Tue Feb 22 2011 - 17:34:19 PST)
- [AMBER] pdb error subrata paul (Tue Feb 22 2011 - 22:46:02 PST)
- [AMBER] nonbonding parameters Jorgen Simonsen (Tue Feb 22 2011 - 23:14:51 PST)
- [AMBER] REDserver {urea molecule} subrata paul (Wed Feb 23 2011 - 03:20:47 PST)
- [AMBER] Calculation of molecular surface for calcium JORGE IULEK (Wed Feb 23 2011 - 03:55:30 PST)
- [AMBER] Principal COORDINATES analysis Massimiliano Porrini (Wed Feb 23 2011 - 04:33:00 PST)
- [AMBER] how to understand disappearing atoms no contribution to DVdl Junjian Miao (Wed Feb 23 2011 - 06:13:45 PST)
- [AMBER] Problem with dihedral angles tommaso.casalini.mail.polimi.it (Wed Feb 23 2011 - 10:09:03 PST)
- [AMBER] Calculation of molecular surface for calcium Jorge Iulek (Wed Feb 23 2011 - 11:14:27 PST)
- [AMBER] sleap bugfixes Scott Brozell (Wed Feb 23 2011 - 13:34:03 PST)
- [AMBER] AMBER specific GPU test drive. Ross Walker (Wed Feb 23 2011 - 18:13:15 PST)
- [AMBER] temperature setting in REMD Cheng-I Lee (Wed Feb 23 2011 - 18:55:32 PST)
- [AMBER] Antechamber - bug Mahmoud A. A. Ibrahim (Wed Feb 23 2011 - 19:25:30 PST)
- [AMBER] High temperature at the beginning A. Gomez-Sicilia (Thu Feb 24 2011 - 01:17:27 PST)
- [AMBER] Protonation of C terminal residue Elisa Frezza (Thu Feb 24 2011 - 02:55:46 PST)
- [AMBER] MMPBSA.py keep_files Jesper Sørensen (Thu Feb 24 2011 - 03:03:04 PST)
- [AMBER] No energy conservation in NVE ensemble amber 11 Ivan Gladich (Thu Feb 24 2011 - 03:49:18 PST)
- [AMBER] Question Beale, John (Thu Feb 24 2011 - 03:39:59 PST)
- [AMBER] chamber colvin (Thu Feb 24 2011 - 04:15:39 PST)
- [AMBER] Open MPI invalid message type 10 Katharina Lang (Thu Feb 24 2011 - 08:21:47 PST)
- [AMBER] (UNKNOWN ATOM TYPE: UA) Jorgen Simonsen (Thu Feb 24 2011 - 13:00:11 PST)
- [AMBER] Explanation of energy "genBorn" column in 3D-RISM calculation? Is solvation free energy computed? Chris King (Thu Feb 24 2011 - 15:15:31 PST)
- [AMBER] MM-PBSA error: Missing BELE for MM in residue 1 Jagur Lambix (Thu Feb 24 2011 - 16:03:38 PST)
- [AMBER] What is the unit for RMSF result? Ashutosh Shandilya (Thu Feb 24 2011 - 20:39:30 PST)
- [AMBER] TI with softcores: size of scmask and crgmask thomas.fox.boehringer-ingelheim.com (Thu Feb 24 2011 - 23:06:10 PST)
- [AMBER] water mediated H-Bond analysis Sangita Kachhap (Fri Feb 25 2011 - 00:32:10 PST)
- [AMBER] sqm out error kala (Fri Feb 25 2011 - 07:42:02 PST)
- [AMBER] improper dihedral torsion parameters for fused rings on tryptophan Sidney Elmer (Fri Feb 25 2011 - 10:37:23 PST)
- [AMBER] Temperature generator of REMD in AMBER? Cheng-I Lee (Fri Feb 25 2011 - 18:22:28 PST)
- [AMBER] how to decide water mediated interaction betwen Sangita Kachhap (Sun Feb 27 2011 - 20:44:31 PST)
- [AMBER] How to defining a bond between the Cβ of the substrate and the Cα of the catalytic serine py (Sun Feb 27 2011 - 21:34:48 PST)
- Re: [AMBER] chamber - resend colvin (Mon Feb 28 2011 - 00:49:09 PST)
- [AMBER] NPT simulation crash using a GPU CARD for a simulation carried out in a organic explicit solvent vitor.felix.ua.pt (Mon Feb 28 2011 - 01:05:25 PST)
- [AMBER] Restart Problem: The results of an integrated simulation and restarted simulations are not equal! Ali M. Naserian-Nik (Mon Feb 28 2011 - 09:56:40 PST)
- Last message date: Mon Feb 28 2011 - 17:00:04 PST
- Archived on: Fri Apr 19 2024 - 05:53:59 PDT
