Amber Archive May 2009: by messages with attachments

[AMBER] unable to start xleap Jayalakshmi Sridhar (Fri May 01 2009 - 11:32:27 PDT)
1. jsridhar.vcf (203 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] QM/MM assigns Cd to C, Se to S C Liu (Sat May 02 2009 - 19:09:27 PDT)
1. cdse.frcmod (346 bytes)
2. cdse.inpcrd (84 bytes)
3. cdse.prmtop (6954 bytes)
4. cdse.pdb (160 bytes)
5. leap.in (211 bytes)
6. ATT00002.txt (137 bytes)
[AMBER] "Parameter file not generated" Remya S R (Sun May 03 2009 - 23:17:23 PDT)
1. BGF.frcmod (1554 bytes)
2. BGF.mol2 (4334 bytes)
3. complex_setup.leapcmd (403 bytes)
4. 227d_dna_BGF.pdb (45018 bytes)
5. ATT00002.txt (137 bytes)
[AMBER] Non-zero internal energy in single trajectory MM-PBSA calculations Dmitry Osolodkin (Mon May 04 2009 - 02:24:59 PDT)
1. snapshot_statistics.out (2162 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] xleap segmentation fault Jayalakshmi Sridhar (Mon May 04 2009 - 08:50:06 PDT)
1. jsridhar.vcf (203 bytes)
2. ATT00002.txt (137 bytes)
Re: [AMBER] Error in PMEMD run Robert Duke (Mon May 04 2009 - 21:08:37 PDT)
1. config_stuff.tar (30720 bytes)
2. ATT00002.txt (137 bytes)
Re: [AMBER] Error in PMEMD run Marek Malý (Wed May 06 2009 - 11:30:43 PDT)
1. configure_amber (44381 bytes)
2. configure (23406 bytes)
3. ATT00002.txt (137 bytes)
Re: [AMBER] Error in PMEMD run Marek Malý (Wed May 06 2009 - 11:42:36 PDT)
1. config.h (1274 bytes)
2. ATT00002.txt (137 bytes)
Re: [AMBER] Error in PMEMD run Marek Malý (Wed May 06 2009 - 11:51:03 PDT)
1. config.h (1274 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] xleap input pdb problem Majeed Shaik (Wed May 06 2009 - 11:47:45 PDT)
1. FLE.mol2 (12471 bytes)
2. FLE.frcmod (686 bytes)
3. oct.pdb (55000 bytes)
4. ATT00002.txt (137 bytes)
RE: [AMBER] QM/MM assigns Cd to C, Se to S Ross Walker (Fri May 08 2009 - 00:16:09 PDT)
1. bugfix.19 (18092 bytes)
2. ATT00002.txt (137 bytes)
Re: [AMBER] Error in PMEMD run Marek Malý (Fri May 08 2009 - 16:37:28 PDT)
1. TEST_FAILURES_AmberTools.diff (1935 bytes)
2. TEST_FAILURES_Amber_PARALLEL_MM.diff (33858 bytes)
3. TEST_FAILURES_AmberSerial_MM.diff (1356 bytes)
4. TEST_FAILURES_AmberSerial_QMMM.diff (545 bytes)
5. ATT00002.txt (137 bytes)
[AMBER] please help me out Nancy (Sun May 10 2009 - 00:56:33 PDT)
1. bundlecc66.pdb (72715 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] The resonable way to create single strand DNA with NAB ? Marek Malý (Sun May 10 2009 - 10:12:09 PDT)
1. GEM91ds_ss.pdb (61146 bytes)
2. GEM91.pdb (60376 bytes)
3. GEM91.png (81878 bytes)
4. ATT00002.txt (137 bytes)
[AMBER] amber9 in fedora10 Bala subramanian (Wed May 13 2009 - 02:50:25 PDT)
1. config.h (3421 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] essential dynamics Chunliyan (Wed May 13 2009 - 09:23:23 PDT)
1. PCA.rar (230161 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] re: essential dynamics Chunliyan (Wed May 13 2009 - 10:25:57 PDT)
1. pca.png (265630 bytes)
2. ATT00002.txt (137 bytes)
RE: [AMBER] re: essential dynamics Niel Henriksen (Wed May 13 2009 - 11:28:22 PDT)
1. CA.pdb (24459 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] Amber 10 install parallel problem Hopkins, Robert (Sat May 16 2009 - 17:38:16 PDT)
1. mkparal.log (576 bytes)
2. config_amber.h (3337 bytes)
3. configure_lam (461 bytes)
4. conflam.log (110015 bytes)
5. ATT00002.txt (137 bytes)
[AMBER] no equilibrium Nancy (Mon May 18 2009 - 19:32:01 PDT)
1. SCC66_md1.in_ (286 bytes)
2. SCC66_md1.out (68673 bytes)
3. SCC66_md2.in (331 bytes)
4. SCC66_md2.out (1452590 bytes)
5. ATT00002.txt (137 bytes)
[AMBER] no equilibrium Nancy (Mon May 18 2009 - 19:44:03 PDT)
1. SCC66_md1.in_ (286 bytes)
2. SCC66_md1.out (68673 bytes)
3. SCC66_md2.in (331 bytes)
4. SCC66_md2.out (1452590 bytes)
5. ATT00002.txt (137 bytes)
Re: [AMBER] Amber - Leap- SolvateBox help Shubhra Gupta (Mon May 18 2009 - 20:54:23 PDT)
1. sugar.pdb (1463 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] Problem with Nmode Kshatresh Dutta Dubey (Mon May 18 2009 - 21:25:05 PDT)
1. mm_pbsa.log (887 bytes)
2. nmode_lig.1.out (1141 bytes)
3. ATT00002.txt (137 bytes)
Re: [AMBER] Problem with nonstandard residues moitrayee.mbu.iisc.ernet.in (Tue May 19 2009 - 06:10:00 PDT)
1. 1QF6_TSB.pdb (846005 bytes)
2. TSB.in (4199 bytes)
3. ATT00002.txt (137 bytes)
Re: [AMBER] Error running MM _PBSA.pl script liuhui (Tue May 19 2009 - 09:15:24 PDT)
1. mm_pbsa_createinput.pm (26719 bytes)
2. ATT00002.txt (137 bytes)
Re: [AMBER] Protein with HETATM, am I doing the right thing nicholus bhattacharjee (Thu May 21 2009 - 09:28:52 PDT)
1. pdb (180553 bytes)
2. po4 (405 bytes)
3. ATT00002.txt (137 bytes)
[AMBER] Segmentation error in Ptraj Kshatresh Dutta Dubey (Fri May 22 2009 - 00:17:27 PDT)
1. ptraj_all.in (465 bytes)
2. ptraj_all_in.out (5090 bytes)
3. ATT00002.txt (137 bytes)
[AMBER] decomposition and alanine scanning 廖青华 (Fri May 22 2009 - 07:13:49 PDT)
1. mm_pbsa.in (13151 bytes)
2. sander_com.1.out (5259 bytes)
3. ATT00002.txt (137 bytes)
Re: [AMBER] Radius for Bromine in MMPBSA calculation john smith (Sun May 24 2009 - 21:52:48 PDT)
1. binding_energy_m12.mmpbsa (8606 bytes)
2. binding_energy_m12.log (1643 bytes)
3. binding_energy_m13.mmpbsa (8606 bytes)
4. binding_energy_m13.log (1643 bytes)
5. ATT00002.txt (137 bytes)
Re: [AMBER] problem with MM-PBSA Thomas Cheatham (Wed May 27 2009 - 17:35:30 PDT)
1. ATT00002.txt (137 bytes)
[AMBER] MM-PBSA nmode statistics Dmitry Osolodkin (Thu May 28 2009 - 04:54:18 PDT)
1. stat.tar.gz (2614 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] xleap segmentation fault Jayalakshmi Sridhar (Thu May 28 2009 - 09:29:47 PDT)
1. jsridhar.vcf (203 bytes)
2. ATT00002.txt (137 bytes)
Re: [AMBER] How to take into account the charge in GAFF parameterization cgji (Thu May 28 2009 - 23:49:44 PDT)
1. ATT00002.txt (137 bytes)
Re: [AMBER] QQD psuedoatom restraints David A. Case (Fri May 29 2009 - 08:18:29 PDT)
1. dist.patch (1783 bytes)
2. ATT00002.txt (137 bytes)
Re: [AMBER] xleap segmentation fault Jayalakshmi Sridhar (Fri May 29 2009 - 08:45:25 PDT)
1. jsridhar.vcf (203 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] Targeted MD and QM/MM Gabriel Urquiza (Fri May 29 2009 - 13:09:31 PDT)
1. leap.log (170786 bytes)
2. ATT00002.txt (137 bytes)
Re: [AMBER] broken Ligand Shubhra Gupta (Fri May 29 2009 - 23:35:46 PDT)
1. a.prmtop (249441 bytes)
2. a.inpcrd (54284 bytes)
3. min.in (129 bytes)
4. a.pdb (101419 bytes)
5. a_min.pdb (85111 bytes)
6. ATT00002.txt (137 bytes)
[AMBER] ERROR in ptrajInitializeState(): Attempting .... Siavoush Dastmalchi (Sat May 30 2009 - 09:06:51 PDT)
1. ATT00002.txt (137 bytes)
[AMBER] RE: ERROR in ptrajInitializeState(): Attempting .... Siavoush Dastmalchi (Sat May 30 2009 - 10:11:55 PDT)
1. ATT00002.txt (137 bytes)
Re: [AMBER] MM-PBSA nmode statistics Dmitry Osolodkin (Sat May 30 2009 - 10:25:46 PDT)
1. 04_MMPBSA_Nmode.tar.gz (7577 bytes)
2. ATT00002.txt (137 bytes)

Amber Archive May 2009 by messages with attachments