Amber Archive Jul 2011 by messages with attachments
777 messages
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Starting
Thu Jun 30 2011 - 18:30:03 PDT,
Ending
Sun Jul 31 2011 - 05:00:05 PDT
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[AMBER] INSTALLATION ERROR ON RED HAT LINUX
Rajabrata Bhuyan
(Thu Jun 30 2011 - 23:13:28 PDT)
amber_failure
(15149 bytes)
Re: [AMBER] dist restraint
e p
(Fri Jul 01 2011 - 22:03:00 PDT)
mdout
(8498 bytes)
[AMBER] dist restraint
e p
(Fri Jul 01 2011 - 22:05:30 PDT)
mdout
(8498 bytes)
Re: [AMBER] Error mmpbsa
John S
(Fri Jul 01 2011 - 22:15:14 PDT)
pbsa.out
(79584 bytes)
[AMBER] DNA simulation
najmul arfin
(Sun Jul 03 2011 - 22:55:38 PDT)
md1.in
(373 bytes)
md2.in
(288 bytes)
mix_min1.in
(143 bytes)
mix_min2.in
(198 bytes)
xleap.log
(114476 bytes)
[AMBER] using sleap to load mol2 files
case
(Mon Jul 04 2011 - 06:15:03 PDT)
mol2.bugfix
(2992 bytes)
Re: [AMBER] regarding per residue wise free energy decomposition
Hirdesh Kumar
(Mon Jul 04 2011 - 22:26:05 PDT)
test.log
(3581 bytes)
[AMBER] Large flcutions in the RMSD deviations upon changing the parameters values of gamma_ln, taup and timesteps ..How a small variation leads to such a larage change??
Rajesh Raju
(Tue Jul 05 2011 - 16:27:58 PDT)
rmsd1.jpeg
(308414 bytes)
RMSD.pdf
(212314 bytes)
[AMBER] AmberTools installation -
Jennifer L. Muzyka
(Wed Jul 06 2011 - 05:18:28 PDT)
07-06_07-55-39.log
(46062 bytes)
07-06_07-55-39.diff
(1353 bytes)
[AMBER] Different trajectories with large difference in RMSD with changing the parameters values of gamma_ln, taup, timesteps and extend of density equilibration
Rajesh Raju
(Wed Jul 06 2011 - 08:59:32 PDT)
rmsd1.jpeg
(308414 bytes)
RMSD.pdf
(212314 bytes)
Re: [AMBER] sander job crashed
Ben Roberts
(Thu Jul 07 2011 - 17:02:30 PDT)
smime.p7s
(2670 bytes)
Re: [AMBER] sander job crashed
Ben Roberts
(Fri Jul 08 2011 - 04:59:23 PDT)
smime.p7s
(3919 bytes)
[AMBER] XLEaP parameters for nonstandard residues
Julia Blum
(Fri Jul 08 2011 - 07:05:51 PDT)
edit.mol2
(8371 bytes)
edit.frcmod
(410 bytes)
c-pf.pdb
(50593 bytes)
Re: [AMBER] XLEaP parameters for nonstandard residues
Julia Blum
(Fri Jul 08 2011 - 09:26:04 PDT)
edit.mol2
(8371 bytes)
edit.frcmod
(410 bytes)
Re: [AMBER] Different trajectories with different RMSD with changing the parameters of gamma_ln, taup, timesteps and extend of density equilibration
Rajesh Raju
(Fri Jul 08 2011 - 13:16:48 PDT)
rmsd.jpeg
(307044 bytes)
RMSD.pdf
(212314 bytes)
Re: [AMBER] Different trajectories with different RMSD with changing the parameters of gamma_ln, taup, timesteps and extend of density equilibration
Rajesh Raju
(Fri Jul 08 2011 - 14:00:07 PDT)
RMSD.pdf
(212314 bytes)
Re: [AMBER] sander job crashed
Ben Roberts
(Mon Jul 11 2011 - 08:24:21 PDT)
smime.p7s
(3919 bytes)
Re: [AMBER] cudaMemcpy GpuBuffer::Upload failed invalid argument
Oliver Kuhn
(Mon Jul 11 2011 - 10:24:45 PDT)
s01.tar.gzip
(963273 bytes)
Re: [AMBER] Ala double mutation scans
Dwight McGee
(Mon Jul 11 2011 - 10:36:58 PDT)
make_crd.in
(283 bytes)
[AMBER] help
xiao fugui
(Mon Jul 11 2011 - 19:16:56 PDT)
part
(5950 bytes)
part
(33302 bytes)
part
(32379 bytes)
part
(222421 bytes)
[AMBER] Antechamber trouble with COA-acyl chain
Erin Kelly
(Tue Jul 12 2011 - 07:59:28 PDT)
sqm.out
(8190 bytes)
Re: [AMBER] Antechamber trouble with COA-acyl chain
Erin Kelly
(Tue Jul 12 2011 - 09:37:15 PDT)
7_12_3F5O_chemdraw3.pdb
(11920 bytes)
Re: [AMBER] zinc parameters
Ben Roberts
(Tue Jul 12 2011 - 10:11:01 PDT)
smime.p7s
(2670 bytes)
Re: [AMBER] problem with type of pdb output.
Ben Roberts
(Tue Jul 12 2011 - 11:51:50 PDT)
smime.p7s
(2670 bytes)
Re: [AMBER] Antechamber trouble with COA-acyl chain
Erin Kelly
(Tue Jul 12 2011 - 12:40:39 PDT)
coh1.pdb
(8932 bytes)
[AMBER] the picture of secstruct and the analysis of Hbond
qiao xue
(Tue Jul 12 2011 - 18:57:54 PDT)
secstruct.jpg
(4792 bytes)
Hbond.jpg
(8902 bytes)
Re: [AMBER] Antechamber trouble with COA-acyl chain
Erin Kelly
(Wed Jul 13 2011 - 07:28:45 PDT)
1.pdb
(6777 bytes)
Re: [AMBER] Antechamber trouble with COA-acyl chain
Erin Kelly
(Wed Jul 13 2011 - 07:53:48 PDT)
1.pdb
(6777 bytes)
coh1.pdb
(8932 bytes)
Re: [AMBER] Antechamber trouble with COA-acyl chain
intra\\sa175950
(Wed Jul 13 2011 - 08:30:20 PDT)
1b_good.pdb
(6679 bytes)
[AMBER] TR: Antechamber trouble with COA-acyl chain
intra\\sa175950
(Wed Jul 13 2011 - 08:34:36 PDT)
1b_good.pdb
(6679 bytes)
ATT00049.txt
(134 bytes)
Re: [AMBER-Developers] [AMBER] Antechamber trouble with COA-acyl chain
David A Case
(Wed Jul 13 2011 - 11:10:44 PDT)
sqm.in
(5381 bytes)
sqm_g09.in
(5175 bytes)
Re: [AMBER] Antechamber trouble with COA-acyl chain
Erin Kelly
(Wed Jul 13 2011 - 12:59:03 PDT)
1_sqmGAUS.pdb
(6681 bytes)
Re: [AMBER] Antechamber trouble with COA-acyl chain
Erin Kelly
(Wed Jul 13 2011 - 13:10:42 PDT)
1_sqmGAUS.mol2
(9824 bytes)
[AMBER] How to make the picture of secstruct and the analysis of Hbond
qiao xue
(Wed Jul 13 2011 - 16:54:10 PDT)
secstruct.jpg
(4792 bytes)
Hbond.jpg
(8902 bytes)
Re: [AMBER] Antechamber trouble with COA-acyl chain
Erin Kelly
(Thu Jul 14 2011 - 07:07:46 PDT)
hco.mol2
(9823 bytes)
Re: [AMBER] How to make the picture of secstruct and the analysis of Hbond
qiao xue
(Fri Jul 15 2011 - 20:21:04 PDT)
hbond.ptraj
(1594 bytes)
hbond.out
(7558 bytes)
Re: [AMBER] nonbond parameter for copper(Ⅱ) ion
Marek Maly
(Sat Jul 16 2011 - 14:47:54 PDT)
AquistToAmber.xls
(21504 bytes)
[AMBER] Tleap problem with save prmtop and inpcrd file. can someone give me advice?
hai wei
(Sun Jul 17 2011 - 00:27:21 PDT)
leap.log
(257187 bytes)
Re: [AMBER] Error in unit 9 inpcrd file
KIRTANA S
(Sun Jul 17 2011 - 19:36:23 PDT)
pmma_500mer.inpcrd
(273834 bytes)
[AMBER] Periodicity in MD simulations
Oliver Kuhn
(Mon Jul 18 2011 - 11:17:35 PDT)
all.NW.c.angle.pdf
(37187 bytes)
Re: [AMBER] PB calculation error when using MMPBSA.py
Bill Miller III
(Tue Jul 19 2011 - 03:28:33 PDT)
focusing.patch
(12580 bytes)
Re: [AMBER] Periodicity in MD simulations
Oliver Kuhn
(Tue Jul 19 2011 - 22:30:43 PDT)
all.NW.c.bond.pdf
(53508 bytes)
[AMBER] Fwd: Periodicity in MD simulations
Oliver Kuhn
(Tue Jul 19 2011 - 23:00:06 PDT)
all.NW.c.bond.pdf
(53508 bytes)
[AMBER] Amber test failure
haris p
(Tue Jul 19 2011 - 23:41:33 PDT)
testlogp2
(76602 bytes)
testlog
(56277 bytes)
[AMBER] Fwd: Periodicity in MD simulations
Oliver Kuhn
(Wed Jul 20 2011 - 00:43:39 PDT)
all.NW.c.bond.pdf
(53508 bytes)
[AMBER] Fwd: Periodicity in MD simulations
Oliver Kuhn
(Wed Jul 20 2011 - 00:51:22 PDT)
all.NW.c.bond.pdf
(53508 bytes)
[AMBER] Urea box: artifacts or just a special distribution?
Na Le Dang
(Wed Jul 20 2011 - 08:57:58 PDT)
Picture_2.png
(424970 bytes)
[AMBER] H-bond vs. time
Beale, John
(Fri Jul 22 2011 - 03:06:46 PDT)
image001.jpg
(23871 bytes)
[AMBER] reproducing a simulation
Xiao Chen
(Fri Jul 22 2011 - 04:34:35 PDT)
20frames.xlsx
(11145 bytes)
Re: [AMBER] problem with addIons in tleap
Wei Chen
(Fri Jul 22 2011 - 11:33:51 PDT)
3ije.tif
(645968 bytes)
[AMBER] configure_error
Carmen Di Giovanni
(Tue Jul 19 2011 - 10:44:37 PDT)
error_snapshot.docx
(796926 bytes)
Re: [AMBER] Error in unit 9 inpcrd file
KIRTANA S
(Mon Jul 18 2011 - 11:44:46 PDT)
_Copy.mol2
(1025745 bytes)
[AMBER] AMBER10 pimd failure on =>16 cores
Andrew Petersen
(Wed Jul 27 2011 - 14:22:02 PDT)
test2.file
(2603 bytes)
spcfw.rst.1
(47465 bytes)
spcfw.top
(112127 bytes)
cmd.in
(313 bytes)
[AMBER] MMPBSA yielding different values when processed with .prepin and .lib file
sunita gupta
(Thu Jul 28 2011 - 01:14:41 PDT)
Lib_file.txt
(9689 bytes)
LI59bDRG.prepin
(6159 bytes)
LI59b.mol2
(7239 bytes)
Re: [AMBER] possible problem with periodic cell
Bruno Rodrigues
(Thu Jul 28 2011 - 14:55:02 PDT)
system.png
(436236 bytes)
Last message date
:
Sun Jul 31 2011 - 05:00:05 PDT
Archived on
: Wed Oct 09 2024 - 05:54:25 PDT
777 messages
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