Amber Archive Sep 2011: by messages with attachments

[AMBER] cpptraj-segmentation fault Praapti Jayaswal (Wed Aug 31 2011 - 23:02:24 PDT)
1. wt.pdb (192857 bytes)
[AMBER] CCA-Phe terminal using Antechamber Sindrila Dutta banik (Thu Sep 01 2011 - 05:39:46 PDT)
1. cca1.pdb (4759 bytes)
2. cca1_h.pdb (9249 bytes)
3. cca1_new.pdb (9249 bytes)
4. sqm.in (6285 bytes)
5. sqm.out (9455 bytes)
Re: [AMBER] SHAKE error help tsurma.umich.edu (Sat Sep 03 2011 - 14:35:49 PDT)
1. cn.mdin (202 bytes)
2. cn.prmtop (275837 bytes)
3. cn.restrt (63959 bytes)
4. extra_pts.f (74544 bytes)
[AMBER] antechamber am1bcc stops with no error message Danny Xu (Mon Sep 05 2011 - 21:37:38 PDT)
1. PEG9_numbered.mol2 (16077 bytes)
2. sqm.out (29915 bytes)
Re: [AMBER] Non standard residue parameterization madhumita das (Mon Sep 05 2011 - 23:15:46 PDT)
1. sample.pdb (893 bytes)
2. mer.frcmod (205 bytes)
Re: [AMBER] Non standard residue parameterization madhumita das (Mon Sep 05 2011 - 23:22:26 PDT)
1. sample.pdb (893 bytes)
2. CYPlib (2471 bytes)
3. mer.frcmod (205 bytes)
[AMBER] problem with MM-PBSA Maryam Hamzehee (Tue Sep 06 2011 - 01:55:41 PDT)
1. binding_energy.pbs.e112 (8216 bytes)
Re: [AMBER] mbondi3 Jason Swails (Tue Sep 06 2011 - 22:36:56 PDT)
1. ChangeParmRadii.py (9443 bytes)
Re: [AMBER] problem with MM-PBSA Maryam Hamzehee (Wed Sep 07 2011 - 10:45:20 PDT)
1. files.rar (3641 bytes)
Re: [AMBER] mbondi3 Jason Swails (Wed Sep 07 2011 - 12:48:41 PDT)
1. ChangeParmRadii.py (9662 bytes)
Re: [AMBER] MPI version of MMPBSA Siavoush Dastmalchi (Thu Sep 08 2011 - 02:05:16 PDT)
1. winmail.dat (4066 bytes)
[AMBER] Fwd: false positive on too large QM region? Brian Radak (Thu Sep 08 2011 - 07:42:56 PDT)
1. IS_protonated.parm7 (432668 bytes)
2. IS_NVT_0.00_1.out (22356 bytes)
Re: [AMBER] Fwd: false positive on too large QM region? Brian Radak (Thu Sep 08 2011 - 13:42:56 PDT)
1. IS_protonated.parm7 (432668 bytes)
2. IS_NVT_0.00_1.inp (1095 bytes)
3. IS_NVT_0.00_1.out (22819 bytes)
Re: [AMBER] how to fill in missing parameters in tleap? Yun Shi (Fri Sep 09 2011 - 16:51:48 PDT)
1. mono.pdb (1734 bytes)
2. mono.gro (1279 bytes)
3. mono.top (14275 bytes)
4. mono.inpcrd (957 bytes)
5. mono.prmtop (18368 bytes)
[AMBER] QM-MM atoms input Shruti Koulgi (Mon Sep 12 2011 - 04:00:58 PDT)
1. wt.pdb (192857 bytes)
Re: [AMBER] cpptraj-segmentation fault Daniel Roe (Mon Sep 12 2011 - 05:52:38 PDT)
1. cpptraj.out (2205 bytes)
2. valgrind.out (792 bytes)
Re: [AMBER] how to fill in missing parameters in tleap? Astrid Maaß (Mon Sep 12 2011 - 06:11:15 PDT)
1. gpt_in (994 bytes)
2. leapin (1491 bytes)
3. glycam_phase_shift.dat (47403 bytes)
4. GLYCAM_06c.dat (47364 bytes)
5. dihedral_profiles.eps (25683 bytes)
Re: [AMBER] pbsa kirtana S (Mon Sep 12 2011 - 11:42:44 PDT)
1. _Copy.out (8438 bytes)
Re: [AMBER] cpptraj-segmentation fault Praapti Jayaswal (Mon Sep 12 2011 - 21:37:17 PDT)
1. log (19 bytes)
2. compilers (586 bytes)
[AMBER] Compiling Amber11 on Blue Gene/P Garo Garabedyan (Tue Sep 13 2011 - 12:45:37 PDT)
1. Mixing-Fortran-and-C-Problem-Repro.tar (10240 bytes)
2. src70.out (75767 bytes)
[AMBER] attachment for my previous mail Fredrick Devadoss (Wed Sep 14 2011 - 07:00:38 PDT)
1. TMD1.in (587 bytes)
2. tmd_plot_RESENE.pdf (395779 bytes)
3. tmd_plot_RMSD.pdf (399930 bytes)
Re: [AMBER] MMPBSA.py 3DRISM error Jason Swails (Wed Sep 14 2011 - 19:09:18 PDT)
1. bugfix.17 (1310 bytes)
Re: [AMBER] how to fill in missing parameters in tleap? Yun Shi (Wed Sep 14 2011 - 22:07:21 PDT)
1. mono.inpcrd (960 bytes)
2. mono.prmtop (18368 bytes)
3. mono_GMX.gro (1280 bytes)
4. mono_GMX.top (18248 bytes)
Re: [AMBER] cpptraj-segmentation fault Praapti Jayaswal (Thu Sep 15 2011 - 21:19:40 PDT)
1. log1.txt (1526 bytes)
Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi (Thu Sep 15 2011 - 21:56:35 PDT)
1. ChargeConstraint.png (24877 bytes)
[AMBER] Serious error (or bug) with free energy decomposition MMPBSA.py..The binding free energy values differs in decomposition analysis.. Rajesh Raju (Sat Sep 17 2011 - 13:43:31 PDT)
1. decompose1.out (7207 bytes)
2. FINAL_DECOMP_MMPBSA.dat (119771 bytes)
3. salt.out (7197 bytes)
Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi (Sun Sep 18 2011 - 21:38:55 PDT)
1. ChargeConstraint1.bmp (512874 bytes)
[AMBER] rst or mdcrd file to view the structures? Chinh Su Tran To (Sun Sep 18 2011 - 22:34:54 PDT)
1. min2.png (69342 bytes)
2. heat7.png (82293 bytes)
3. heat7_crd.png (81534 bytes)
4. md1.png (77296 bytes)
5. md1_crd.png (50270 bytes)
6. md1_crd_zoom.png (201216 bytes)
7. md11.png (57734 bytes)
8. md11_crd_zoom.png (117595 bytes)
Re: [AMBER] iAPBS 1.2.0 - APBS 1.0.0 - Amber11 compilation error Jason Swails (Mon Sep 19 2011 - 15:22:23 PDT)
1. patch.apbs (677 bytes)
Re: [AMBER] Instantaneous temperature in TI simulation Brian Radak (Tue Sep 20 2011 - 07:59:36 PDT)
1. temp_diff.ps (52178 bytes)
Re: [AMBER] Xleap Installation Ben Roberts (Wed Sep 21 2011 - 06:51:05 PDT)
1. smime.p7s (4373 bytes)
[AMBER] problem with nmodes calculation-260-residue protein hongphuc nguyen (Fri Sep 23 2011 - 02:15:37 PDT)
1. dexan-1.png (8024 bytes)
[AMBER] fixing rmsd values Massimiliano Porrini (Sun Sep 25 2011 - 08:22:13 PDT)
1. tetra_rmsd.jpg (33598 bytes)
[AMBER] GAMESS to RESP input file shome sankar bhunia (Mon Sep 26 2011 - 03:46:25 PDT)
1. resp2_csh.csh (4147 bytes)
Re: [AMBER] fixing rmsd values Massimiliano Porrini (Mon Sep 26 2011 - 07:46:52 PDT)
1. rmsd.jpg (37744 bytes)
Re: [AMBER] fixing rmsd values Massimiliano Porrini (Mon Sep 26 2011 - 10:18:47 PDT)
1. rmsd.jpg (38794 bytes)
Re: [AMBER] RMSD fatahiya (Mon Sep 26 2011 - 19:08:39 PDT)
1. 2JUQ.pdb (16606 bytes)
2. md91.pdb (14161 bytes)
Re: [AMBER] dihedral parameters Jason Swails (Tue Sep 27 2011 - 05:01:07 PDT)
1. scan.sh (2705 bytes)
Re: [AMBER] Mol2 file creation Chidambar Kulkarni (Tue Sep 27 2011 - 09:05:04 PDT)
1. ANTECHAMBER_AC.AC (21553 bytes)
2. ANTECHAMBER_AC.AC0 (21553 bytes)
3. ANTECHAMBER_AM1BCC_PRE.AC (12288 bytes)
4. ANTECHAMBER_BOND_TYPE.AC (21553 bytes)
5. ANTECHAMBER_BOND_TYPE.AC0 (21553 bytes)
6. ATOMTYPE.INF (37905 bytes)
7. sqm.in (10497 bytes)
8. sqm.out (34764 bytes)
[AMBER] Fwd: fixing rmsd values (follow-up) Massimiliano Porrini (Tue Sep 27 2011 - 11:44:14 PDT)
1. rmsd.jpg (38794 bytes)
Re: [AMBER] Fwd: fixing rmsd values (follow-up) Massimiliano Porrini (Wed Sep 28 2011 - 11:10:52 PDT)
1. rmsd.jpg (42251 bytes)
[AMBER] sander mpi error when unfolding the protein Chinh Su Tran To (Thu Sep 29 2011 - 00:43:24 PDT)
1. heat3.png (106808 bytes)

Amber Archive Sep 2011 by messages with attachments