Amber Archive Aug 2011: by messages with attachments

[AMBER] loadPdb segmentation fault Massimiliano Porrini (Mon Aug 01 2011 - 09:18:51 PDT)
1. seh.library (2616 bytes)
[AMBER] About running sander parallel Aimin (Mon Aug 01 2011 - 11:04:36 PDT)
1. 07-29_17-14-20.diff (157449 bytes)
2. 07-29_17-14-20.log (324559 bytes)
Re: [AMBER] About running sander parallel Aimin (Mon Aug 01 2011 - 16:41:52 PDT)
1. 08-01_11-16-21.diff (157869 bytes)
2. 08-01_11-16-21.log (324660 bytes)
Re: [AMBER] About running sander parallel Aimin (Mon Aug 01 2011 - 18:07:28 PDT)
1. cpuinfo.txt (16740 bytes)
Re: [AMBER] loadPdb segmentation fault Massimiliano Porrini (Tue Aug 02 2011 - 13:42:10 PDT)
1. peptide.pdb (9591 bytes)
2. seh.library (2616 bytes)
Re: [AMBER] loadPdb segmentation fault Jason Swails (Tue Aug 02 2011 - 21:38:22 PDT)
1. seh.mod.off (2603 bytes)
[AMBER] 6 error: No torsion terms for ca-ca-ce-c2 Shulin Zhuang (Thu Aug 04 2011 - 09:03:51 PDT)
1. lig.pdb (1454 bytes)
2. new.frcmod (578 bytes)
[AMBER] 1st shell WITH solvent in ptraj Bruno Rodrigues (Thu Aug 04 2011 - 16:02:07 PDT)
1. pdb_1st_shell.out (1694 bytes)
[AMBER] Error in output file Aditya Padhi (Fri Aug 05 2011 - 02:55:38 PDT)
1. Error.txt (848 bytes)
Re: [AMBER] simulating a protein-peptide complex Xiao Chen (Fri Aug 05 2011 - 02:36:03 PDT)
1. ligand-complex-15ns-rmsd.xls (65024 bytes)
[AMBER] Amoeba seems not work with free energy calculation li he (Fri Aug 05 2011 - 13:06:21 PDT)
1. Na_solvation_amoeba.tar (507358 bytes)
[AMBER] Amber 11 parallel installation problem 于丽影 Liying E\. Yu (Fri Aug 05 2011 - 18:30:16 PDT)
1. make.log (102729 bytes)
2. config.h (5360 bytes)
Re: [AMBER] How to know whether the sander is running parallel Aimin (Sat Aug 06 2011 - 20:54:57 PDT)
1. equil10.rar (312068 bytes)
Re: [AMBER] Chemical shift restraints Siavoush Dastmalchi (Sat Aug 06 2011 - 23:54:31 PDT)
1. winmail.dat (5866 bytes)
Re: [AMBER] Chemical shift restraints Siavoush Dastmalchi (Sun Aug 07 2011 - 07:01:18 PDT)
1. winmail.dat (4006 bytes)
Re: [AMBER] Chemical shift restraints Siavoush Dastmalchi (Sun Aug 07 2011 - 07:02:08 PDT)
1. winmail.dat (4350 bytes)
Re: [AMBER] Chemical shift restraints Siavoush Dastmalchi (Sun Aug 07 2011 - 07:05:16 PDT)
1. winmail.dat (4386 bytes)
[AMBER] DNA-22mer manikanthan bhavaraju (Mon Aug 08 2011 - 13:37:13 PDT)
1. DNA_aptamer.pdb (38712 bytes)
[AMBER] Inpcrd file problem David Cantu (Thu Aug 11 2011 - 07:53:06 PDT)
1. m1.out (2779 bytes)
Re: [AMBER] loadpdb with GLYCAM_06 ? Yun Shi (Mon Aug 15 2011 - 11:32:09 PDT)
1. 330.gif (96 bytes)
[AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi (Tue Aug 16 2011 - 11:34:59 PDT)
1. tri.png (18748 bytes)
Re: [AMBER] Old problem with restart Bruno Rodrigues (Tue Aug 16 2011 - 13:22:40 PDT)
1. system.png (436236 bytes)
[AMBER] NOE constraints labeling marco.bartoloni.students.unibe.ch (Thu Aug 18 2011 - 03:55:32 PDT)
1. rOe_distance_restraint_refinement_protocol.doc (26112 bytes)
Re: [AMBER] ntr=1 nmropt=1 Fernando Martín García (Fri Aug 19 2011 - 03:52:14 PDT)
1. ftsa_cter_std1.in (413 bytes)
Re: [AMBER] Using iwrap with harmonic restraints Ozen, Aysegul (Mon Aug 22 2011 - 17:27:31 PDT)
1. date_ (27441 bytes)
2. date_ (27441 bytes)
[AMBER] About sudden simulation box twist Bin Wu (Tue Aug 23 2011 - 13:53:10 PDT)
1. 2.gif (733321 bytes)
Re: [AMBER] antechamber error vaibhav dixit (Thu Aug 25 2011 - 01:15:19 PDT)
1. sqm.out (6584 bytes)
Re: [AMBER] ptraj invalid writes Ben Gamari (Thu Aug 25 2011 - 12:29:49 PDT)
1. ptraj.stdout (125868 bytes)
2. ptraj.stderr (0 bytes)
3. ptraj.fail (3634 bytes)
4. runptraj_y (23381 bytes)
Re: [AMBER] antechamber error vaibhav dixit (Thu Aug 25 2011 - 22:50:43 PDT)
1. VD69_1.prep (6047 bytes)
[AMBER] folding/unfolding or just local minimum trap? Chinh Su Tran To (Fri Aug 26 2011 - 03:16:11 PDT)
1. rms_to_457.png (14246 bytes)
[AMBER] problem with Cadmium parameters and running minimization Hashem Taha (Fri Aug 26 2011 - 07:57:27 PDT)
1. 1JGM_CD_chg1.prep (12168 bytes)
2. 1JGM_CD_sem.frcmod (2359 bytes)
3. 1JGM_CD_sol.minwat.out (10818 bytes)
4. 1JGM_CD.pqr (357109 bytes)
5. leap.in (703 bytes)
6. minwat.inp (142 bytes)
7. metals.frcmod (400 bytes)
Re: [AMBER] problem with Cadmium parameters and running minimization Ben Roberts (Fri Aug 26 2011 - 08:01:37 PDT)
1. smime.p7s (2670 bytes)
Re: [AMBER] problem with Cadmium parameters and running minimization Ben Roberts (Fri Aug 26 2011 - 08:13:37 PDT)
1. smime.p7s (2670 bytes)
Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi (Fri Aug 26 2011 - 11:08:06 PDT)
1. demo.bmp (455358 bytes)
[AMBER] how to fill in missing parameters in tleap? Yun Shi (Fri Aug 26 2011 - 18:01:25 PDT)
1. demo.bmp (455358 bytes)
Re: [AMBER] antechamber error vaibhav dixit (Fri Aug 26 2011 - 22:34:45 PDT)
1. sqm.in (3845 bytes)
Re: [AMBER] antechamber error case (Sun Aug 28 2011 - 06:45:03 PDT)
1. sqm.out (49348 bytes)
[AMBER] PBS script Bruno Rodrigues (Mon Aug 29 2011 - 13:05:41 PDT)
1. 08-29_14-48-17.log (64324 bytes)
Re: [AMBER] Ptraj and wrapping water molecules Ozen, Aysegul (Tue Aug 30 2011 - 12:07:49 PDT)
1. date_ (211489 bytes)
Re: [AMBER] problem in installing xleap David A Case (Wed Aug 31 2011 - 05:29:10 PDT)
1. ubuntu_xleap.patch (1447 bytes)
Re: [AMBER] Ptraj and wrapping water molecules Sai Kumar Ramadugu (Wed Aug 31 2011 - 13:32:23 PDT)
1. snapshot.pdf (186413 bytes)

Amber Archive Aug 2011 by messages with attachments