Amber Archive Mar 2010: by messages with attachments

[AMBER] parameter file for modified nucleosides (O6-methyl guanine) N.R. Jena (Tue Mar 02 2010 - 04:24:59 PST)
1. 11.pdb (213218 bytes)
[AMBER] parameter file for modified nucleosides (O6-methyl guanine) N.R. Jena (Tue Mar 02 2010 - 04:53:39 PST)
1. 11.pdb (213218 bytes)
Re: [AMBER] parameter file for modified nucleosides (O6-methyl guanine) N.R. Jena (Tue Mar 02 2010 - 08:59:38 PST)
1. 6OG.prepin.txt (3178 bytes)
2. 6OG.frcmod.txt (10522 bytes)
[AMBER] Segmentation fault Asfa Ali (Wed Mar 03 2010 - 07:20:28 PST)
1. leap.log (30733 bytes)
Re: [AMBER] atom-type cz ??? Barbault Florent (Wed Mar 03 2010 - 07:59:58 PST)
1. prep.prep (2300 bytes)
2. pdb_input.pdb (1321 bytes)
[AMBER] neb/amber 10 Guillermina Estiu (Wed Mar 03 2010 - 11:12:05 PST)
1. gestiu.vcf (249 bytes)
[AMBER] sleap help InSuk Joung (Thu Mar 04 2010 - 13:55:15 PST)
1. leap.in (135 bytes)
2. test.pdb (1543 bytes)
[AMBER] ERROR: PGFIO-F-239/namelist read/unit=5/entity name is not member of group. lee lior (Tue Mar 09 2010 - 13:41:51 PST)
1. MD.in (466 bytes)
2. RC.4.FC30.o1278140 (1832 bytes)
3. NoLoop.pbs (834 bytes)
[AMBER] MMPBSA in case of highly water accessible molecules ? Marek Maly (Tue Mar 09 2010 - 13:43:11 PST)
1. den_al.tif (492242 bytes)
[AMBER] problem to generate parameters files of DNA Ananya Paul (Wed Mar 10 2010 - 02:18:28 PST)
1. hy.pdb (77873 bytes)
Re: [AMBER] problem to generate parameters files from NMR solved DNA structure Ananya Paul (Thu Mar 11 2010 - 05:40:54 PST)
1. leap.log (95903 bytes)
[AMBER] tleap and xleap problem in loading mol2 files d96543015.ntu.edu.tw (Thu Mar 11 2010 - 20:51:41 PST)
1. db2clean01.mol2 (9945 bytes)
2. db2_clean01.pdb (7790 bytes)
[AMBER] Enquiry regarding Minimisation Pallavi Mohanty (Sat Mar 13 2010 - 02:50:22 PST)
1. min.txt (11885 bytes)
[AMBER] regarding NMR structures Asfa Ali (Tue Mar 16 2010 - 06:08:20 PDT)
1. 143D.pdb (367902 bytes)
[AMBER] problem in minimisation Hyma vathi (Wed Mar 17 2010 - 08:04:12 PDT)
1. NAP.mol2 (6503 bytes)
2. ZST.mol2 (5019 bytes)
Re:Re: [AMBER] PBSOL not equal to PBSUR + PBCAL? Jeffrey (Thu Mar 18 2010 - 18:41:51 PDT)
1. snapshot_statistics.out (2125 bytes)
2. snapshot_statistics.out.snap (166374 bytes)
3. snapshot_com.all.out (91838 bytes)
4. snapshot_rec.all.out (91838 bytes)
5. binding.out (68230 bytes)
6. snapshot_lig.all.out (91838 bytes)
Re: Re: [AMBER] error when doing MMPBSA pxq (Mon Mar 22 2010 - 01:51:44 PDT)
1. output1 (31725 bytes)
Re: Re: [AMBER] error when doing MMPBSA pxq (Mon Mar 22 2010 - 17:32:42 PDT)
1. A_rec.all.out (142234 bytes)
2. A_com.all.out (175246 bytes)
[AMBER] mmpbsa doesn't work qiaoyan (Mon Mar 22 2010 - 20:38:48 PDT)
1. SA.out.out (504 bytes)
2. SA.in.in (175 bytes)
[AMBER] problem with antechamber for C60 Chun-Wei Pao (Mon Mar 22 2010 - 20:47:00 PDT)
1. fullerene2.pdb (4304 bytes)
[AMBER] problem with antechamber for C60 Chun-Wei Pao (Mon Mar 22 2010 - 23:10:59 PDT)
1. fullerene2.pdb (4303 bytes)
[AMBER] Solvatebox on Amber8 pellegrini (Tue Mar 23 2010 - 03:29:32 PDT)
1. ADA.pdb (5022 bytes)
[AMBER] Problem with solvationbox command pellegrini (Tue Mar 23 2010 - 06:11:17 PDT)
1. ADA.pdb (5022 bytes)
2. ADA_Solvated.pdb (392534 bytes)
Re: Re: Re: [AMBER] error in save prmtop geyan (Tue Mar 23 2010 - 07:44:12 PDT)
1. pro.pdb (90933 bytes)
2. leap.log (2055 bytes)
Re: [AMBER] problem with antechamber for C60 Dean Cuebas (Tue Mar 23 2010 - 13:13:37 PDT)
1. fullerene.mol2 (6873 bytes)
2. fullerene2.mol2 (6778 bytes)
3. fullerene2.frc (301 bytes)
[AMBER] ligand parameterization gurunath katagi (Tue Mar 23 2010 - 23:05:24 PDT)
1. NCI445.pdb_ligand_01.pdbqt (3207 bytes)
2. lig2.pdb (3796 bytes)
3. c2.pdb (164956 bytes)
[AMBER] Missing values for MM BGAS:error in mm-pbsa moitrayee.mbu.iisc.ernet.in (Wed Mar 24 2010 - 11:53:26 PDT)
1. c.pdb (760878 bytes)
Re: [AMBER] Energy units in mm-pbsa calculations moitrayee.mbu.iisc.ernet.in (Thu Mar 25 2010 - 09:42:10 PDT)
1. decomp.in (5671 bytes)
2. ubi_com.all.out (1230299 bytes)
Re: [AMBER] MMPBSA error Soumya Lipsa Rath (Thu Mar 25 2010 - 20:43:08 PDT)
1. snapshot_com.all.out (17503 bytes)
2. snapshot_lig.all.out (17503 bytes)
3. snapshot_rec.all.out (17503 bytes)
Re: [AMBER] Energy units in mm-pbsa calculations moitrayee.mbu.iisc.ernet.in (Fri Mar 26 2010 - 05:34:41 PDT)
1. mm_pbsa.in (7185 bytes)
Re: [AMBER] Post-processing with AMBER 10 Daniel Roe (Fri Mar 26 2010 - 14:31:51 PDT)
1. amber10.imin5.patch (12392 bytes)
[AMBER] MM-PBSA not generating snapshot_lig.all.out and snapshot_statistics.out files mish (Sat Mar 27 2010 - 11:25:49 PDT)
1. extract_coords.mmpbsa (822 bytes)
2. binding_energy.mmpbsa (1066 bytes)
3. snapshot_rec.all.out (84 bytes)
4. snapshot_com.all.out (139752 bytes)
5. binding_energy.log (33766 bytes)
RE: [AMBER] Amber:antechamber & heme(metal?) problems Shaikh Abdul R S Ramaju (Sun Mar 28 2010 - 23:00:11 PDT)
1. heme_final.prep (0 bytes)
2. HEME.pdb (0 bytes)
3. heme_final.dat (0 bytes)
Re: Re: [AMBER] minimization really make protein better? geyan (Mon Mar 29 2010 - 20:15:55 PDT)
1. minimized.ps (51493 bytes)
2. initial.pdb (90933 bytes)
3. initial.ps (51481 bytes)
4. minimized.pdb (90933 bytes)
[AMBER] how to convert to standard Amber PDB input geyan (Mon Mar 29 2010 - 20:26:17 PDT)
1. ABC_com.pdb (310666 bytes)
[AMBER] (no subject) Nicee (Mon Mar 29 2010 - 21:31:51 PDT)
1. md1.in (3218 bytes)
2. model_noref_3g5a_md1.out (338195 bytes)
[AMBER] vlimit error during equilibration step Nicee (Mon Mar 29 2010 - 21:37:28 PDT)
1. md1.in (3218 bytes)
2. model_noref_3g5a_md1.out (338195 bytes)
Re:Re: [AMBER] is iwrap=1 a key parameter? Nancy (Mon Mar 29 2010 - 22:11:17 PDT)
1. 4ns.jpg (59597 bytes)
2. xrd_villin_.jpg (86858 bytes)
[AMBER] QMMM of protein-ligand complex: Unable to achieve self consistency Dmitri Nilov (Tue Mar 30 2010 - 07:41:00 PDT)
1. min1_qmmm.in (568 bytes)
2. ligand.pdb (3198 bytes)
[AMBER] COOH group:extra undesired bond Jio M (Wed Mar 31 2010 - 09:41:06 PDT)
1. hf631_all.mol2 (2353 bytes)
2. hf631.mol2 (2353 bytes)
3. cep_all.mol2 (2353 bytes)
4. cep.mol2 (2353 bytes)

Amber Archive Mar 2010 by messages with attachments