Amber Archive Feb 2012 by messages with attachments
641 messages
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Starting
Tue Jan 31 2012 - 22:30:02 PST,
Ending
Wed Feb 29 2012 - 14:30:02 PST
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Re: [AMBER] MMPBSA problem
Urszula Uciechowska
(Wed Feb 01 2012 - 00:02:35 PST)
LIG.prmtop
(80247 bytes)
L_lig.crd.1
(6329 bytes)
Re: [AMBER] NMODE list index out of range error
Sangeetha B
(Wed Feb 01 2012 - 20:18:27 PST)
MMPBSA_nm.zip
(287072 bytes)
Re: [AMBER] Fwd: about using MMPBSA Tan and Luo method in AMBER 11: discrepancy in ECAVITY values
Qin Cai
(Thu Feb 02 2012 - 12:33:57 PST)
patch_ecavity
(738 bytes)
[AMBER] Charge calculation using RESP: MCPB
kanika singal
(Mon Feb 06 2012 - 04:06:04 PST)
1fx7_ms2_large_mk.log
(373692 bytes)
1fx7_ms2_chg1.xml
(66707 bytes)
1fx7_ms2_large_mk1.resp2.chg
(932 bytes)
1fx7_ms2_large.pdb
(5067 bytes)
[AMBER] pmemd test failure when compiling with intel 12.1.2
Vlad Cojocaru
(Mon Feb 06 2012 - 07:22:52 PST)
test_a_serial.log
(100063 bytes)
[AMBER] Fwd: NMODE list index out of range error
Sangeetha B
(Tue Feb 07 2012 - 03:52:42 PST)
MMPBSA_nm.zip
(287072 bytes)
[AMBER] error in tleap execution of loadpdb
molguin.miners.utep.edu
(Tue Feb 07 2012 - 22:09:48 PST)
NEWPDB.PDB
(4951 bytes)
pyrolle.frcmod
(1058 bytes)
pyrolle.prep
(7621 bytes)
tleap.log
(9054 bytes)
Test.pdb
(4951 bytes)
Re: [AMBER] AMBER minimization
Olena Dobrovolska
(Wed Feb 08 2012 - 04:19:21 PST)
P1.min.out
(117547 bytes)
RST.dist
(28279 bytes)
Re: [AMBER] Force Field Parameterization -- Torsion Potentials
Karl N. Kirschner
(Wed Feb 08 2012 - 05:11:55 PST)
Relative_Energy_all.ps
(23082 bytes)
[AMBER] Fwd: Residue Decomposition Sander Error
Hirdesh Kumar
(Thu Feb 09 2012 - 20:33:37 PST)
_MMPBSA_pb_decomp_com.mdin
(352 bytes)
_MMPBSA_pb_decomp_lig.mdin
(292 bytes)
_MMPBSA_pb_decomp_rec.mdin
(298 bytes)
Re: [AMBER] Generating topology files for non standard amino acid residue
Matthew D Antalek
(Mon Feb 13 2012 - 20:55:34 PST)
3fY_2.ac
(2959 bytes)
mainchain.3fY
(386 bytes)
Re: [AMBER] md stopping in TI calculation
leila karami
(Tue Feb 14 2012 - 01:12:08 PST)
free_tg_1_min_v0_0.1.out
(18244 bytes)
free_tg_1_min_v1_0.1.out
(18803 bytes)
Re: [AMBER] ptraj analysis
Giachetti Andrea - CERM
(Tue Feb 14 2012 - 07:40:06 PST)
distance.jpg
(14587 bytes)
Re: [AMBER] Change the residue number in pdb file
Jan-Philip Gehrcke
(Wed Feb 15 2012 - 06:46:51 PST)
renumber_pdb_residues.py
(5617 bytes)
Re: [AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint."
David A Case
(Thu Feb 16 2012 - 06:33:07 PST)
sander_restraint_parse_testcase.tar.gz
(477420 bytes)
[AMBER] Ligands fly away from binding pocket
tian zhu
(Sun Feb 19 2012 - 15:30:35 PST)
min_sol.in
(152 bytes)
min_all.in
(99 bytes)
heat.in
(340 bytes)
density.in
(258 bytes)
equil.in
(293 bytes)
prod.in
(204 bytes)
[AMBER] Antechamber
Beale, John
(Mon Feb 20 2012 - 02:04:32 PST)
image001.jpg
(23871 bytes)
Re: [AMBER] Problem building octahedral coordinated ligands in LEaP
Jesper Sørensen
(Mon Feb 20 2012 - 10:38:54 PST)
frcmod.dummymg
(1212 bytes)
md6.off
(1913 bytes)
example.tleap
(344 bytes)
[AMBER] Charges
Beale, John
(Tue Feb 21 2012 - 02:11:32 PST)
image001.jpg
(23871 bytes)
Re: [AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW
JiYuan Liu
(Tue Feb 28 2012 - 01:16:04 PST)
backbone_rmsd.png
(35888 bytes)
density.png
(23987 bytes)
temp.png
(22902 bytes)
total_energy.png
(24310 bytes)
backbone_rmsd.png
(40437 bytes)
density.png
(44535 bytes)
temp.png
(50032 bytes)
total_energy.png
(68785 bytes)
ca1.pdb
(2133 bytes)
ca.pdb
(1485 bytes)
Re: [AMBER] strip and use of distance-based mask
Nanna Holmgaard List
(Wed Feb 29 2012 - 08:32:48 PST)
distancemask.tar.gz
(452868 bytes)
Last message date
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Wed Feb 29 2012 - 14:30:02 PST
Archived on
: Fri Oct 04 2024 - 05:54:29 PDT
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