Amber Archive Feb 2013: by messages with attachments

[AMBER] Problem using solvatebox for large, linear peptide Joe Passman (Thu Jan 31 2013 - 18:16:09 PST)
1. BoxLength20.jpg (92170 bytes)
2. BoxLength60.jpg (109498 bytes)
[AMBER] average structure Urszula Uciechowska (Fri Feb 01 2013 - 02:31:55 PST)
1. average.png (22860 bytes)
Re: [AMBER] density calculation in radial cpptraj Asmita Gupta (Wed Feb 06 2013 - 00:21:23 PST)
1. rdf_na_bin_50.eps (9473 bytes)
[AMBER] issues with PDB file and tleap Massimiliano Porrini (Thu Feb 07 2013 - 03:45:58 PST)
1. leap.log (42089 bytes)
2. tleap.out (3468 bytes)
Re: [AMBER] problem with 3-ring system in antechamber David A Case (Fri Feb 08 2013 - 10:53:32 PST)
1. threer.mol2 (2694 bytes)
[AMBER] PSF file, atom radii and chamber Massimiliano Porrini (Mon Feb 11 2013 - 10:05:48 PST)
1. chamber.out (2786 bytes)
Re: [AMBER] Cannot open the input file: XYZ.pdb in rpdb(), exit Matthias Leeder (Thu Feb 14 2013 - 01:43:20 PST)
1. Log.7z (9869 bytes)
[AMBER] Fwd: PSF file, atom radii and chamber Massimiliano Porrini (Mon Feb 18 2013 - 01:04:46 PST)
1. chamber.out (2786 bytes)
[AMBER] problem in nmode Rasha Alqus (Wed Feb 20 2013 - 06:39:39 PST)
1. G17nabPAR.job (160 bytes)
2. G17nabPAR.job.e35922 (758 bytes)
3. G17nabSER.job (129 bytes)
4. G17nabSER.job.e35920 (148 bytes)
5. vac-nmode.in (492 bytes)
Re: [AMBER] problem reading CHARMM lipid parameters into chamber Jason Swails (Thu Feb 21 2013 - 04:25:47 PST)
1. chamber.patch (984 bytes)
[AMBER] amber error about protein containing heme tianchuan1015 (Thu Feb 21 2013 - 23:58:31 PST)
1. R.pdb (313442 bytes)
2. frcmod.hemall (2947 bytes)
3. heme_all.in (7133 bytes)
4. R.frcmod (1368 bytes)
Re: [AMBER] amber error about protein containing heme Prajwal Nandekar (Fri Feb 22 2013 - 01:42:17 PST)
1. heme_all.frcmod (3592 bytes)
2. heme_all.prepin (7093 bytes)
[AMBER] ligand moving out of protein incorrect imaging of trajectory using image and center commands with amber 10 ET (Fri Feb 22 2013 - 10:10:20 PST)
1. 3c6-Hbond-Distance.jpg (63085 bytes)
2. ols_RAWComplex_DistanceFin.jpg (568826 bytes)
[AMBER] dihedral distribution plot colvin (Sun Feb 24 2013 - 21:33:06 PST)
1. D1D2.png (57291 bytes)
[AMBER] mmgbsa minimisation failing with error in trajene() ET (Mon Feb 25 2013 - 04:42:14 PST)
1. GS4_ASP25_complex.zip (533300 bytes)
Re: [AMBER] problem in running MMPBSA Saugata Hazra (Mon Feb 25 2013 - 15:20:51 PST)
1. leap.log.doc (114688 bytes)
2. mmpbsa_error_msg.doc (11776 bytes)
3. atp.pdb (2511 bytes)
4. atp_mg_vac.inpcrd (1626 bytes)
5. atp_mg_vac.prmtop (32847 bytes)
6. mg.pdb (79 bytes)
[AMBER] error in nmode Rasha Alqus (Tue Feb 26 2013 - 08:46:16 PST)
1. vac-nmode.in (491 bytes)
2. vac-nmode.sh.e36040 (4244 bytes)
3. vac-nmode.sh (384 bytes)
Re: [AMBER] Building a new structure! Ibrahim Said (Tue Feb 26 2013 - 10:45:20 PST)
1. FLY.off (6142 bytes)
2. protein.pdb (157221 bytes)
[AMBER] error in nmode Rasha Alqus (Wed Feb 27 2013 - 07:03:03 PST)
1. vac-nmode.nab (491 bytes)
[AMBER] aMD Beale, John (Thu Feb 28 2013 - 05:27:17 PST)
1. image001.jpg (23871 bytes)

Amber Archive Feb 2013 by messages with attachments