Amber Archive Apr 2020 by messages with attachments
358 messages
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Starting
Tue Mar 31 2020 - 15:30:02 PDT,
Ending
Thu Apr 30 2020 - 20:30:02 PDT
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Re: [AMBER] Abasic Site and Leap Polymerization
Christina Bergonzo
(Sat Apr 04 2020 - 09:42:11 PDT)
test.ABB.pdb
(50137 bytes)
test.pdb
(60046 bytes)
Re: [AMBER] Abasic Site and Leap Polymerization
Robert Molt
(Sat Apr 04 2020 - 13:01:13 PDT)
bi6024269.pdf
(591576 bytes)
[AMBER] Ligand leaving binding site at high lambdas using TI softcore
Juraj Dobias
(Wed Apr 08 2020 - 13:39:52 PDT)
equil1.in
(599 bytes)
equil2.in
(599 bytes)
equil3.in
(753 bytes)
equil4.in
(752 bytes)
heat.in
(750 bytes)
min.in
(336 bytes)
prod.in
(522 bytes)
[AMBER] questions about paramfit
ttz
(Thu Apr 09 2020 - 21:54:12 PDT)
5_mem_ring.prmtop
(19336 bytes)
cft_all_structures.mdcrd
(70088 bytes)
fit_output_ene.dat2
(6293 bytes)
initil_fit.out
(25867 bytes)
job.fit.in
(598 bytes)
sorted_ene.dat
(2035 bytes)
[AMBER] Why is 360 degree is not equal to 0 degree in PES Scan?
Erdem Yeler
(Fri Apr 10 2020 - 16:01:59 PDT)
image.png
(49104 bytes)
Re: [AMBER] Amber18 compiled with GCC/8.3.0 fails some DPFP tests
Cong Liu
(Sat Apr 11 2020 - 07:25:07 PDT)
04-11_at_10.22.57.png
(69304 bytes)
[AMBER] geometry of amino
Song Hu
(Mon Apr 13 2020 - 22:59:00 PDT)
image003.png
(3972 bytes)
image006.jpg
(8710 bytes)
Re: [AMBER] Amber18 compiled with GCC/8.3.0 fails some DPFP tests
Cong Liu
(Tue Apr 14 2020 - 08:24:37 PDT)
04-11_at_10.22.57.png
(69304 bytes)
Re: [AMBER] Amber18 compiled with GCC/8.3.0 fails some DPFP tests
Cong Liu
(Tue Apr 14 2020 - 11:04:08 PDT)
04-11_at_10.22.57.png
(69304 bytes)
Re: [AMBER] Can I use paramfit for MM scan?
Erdem Yeler
(Wed Apr 15 2020 - 14:26:08 PDT)
image.png
(10213 bytes)
x.inpcrd
(598 bytes)
x.prmtop
(12618 bytes)
Re: [AMBER] Interaction of cellulose-hemicellulose
Pinky Mazumder
(Thu Apr 16 2020 - 22:58:54 PDT)
04-17_00-50-31.png
(272771 bytes)
Re: [AMBER] Interaction of cellulose-hemicellulose
Pinky Mazumder
(Fri Apr 17 2020 - 00:45:28 PDT)
hema.pdb
(21580 bytes)
cell.pdb
(20986 bytes)
Re: [AMBER] Interaction of cellulose-hemicellulose
Pinky Mazumder
(Sun Apr 19 2020 - 22:05:17 PDT)
after_loaded_it_xleap.PNG
(7942 bytes)
converted_hemi_vmd.PNG
(77051 bytes)
Re: [AMBER] Interaction of cellulose-hemicellulose
Lachele Foley
(Sun Apr 19 2020 - 23:48:13 PDT)
hema_TER.pdb
(21588 bytes)
Re: [AMBER] Interaction of cellulose-hemicellulose
Pinky Mazumder
(Mon Apr 20 2020 - 18:30:07 PDT)
check_hema.PNG
(5402 bytes)
[AMBER] Problem in calculating pairwise interaction with CPPTRAJ
Prathit Chatterjee
(Tue Apr 21 2020 - 02:47:42 PDT)
image.png
(278756 bytes)
image.png
(291926 bytes)
[AMBER] Restraint on certain atoms during MD
Debarati DasGupta
(Tue Apr 21 2020 - 05:45:15 PDT)
7FE26FD78D404D799A14AED71EA08EDA.png
(38552 bytes)
Re: [AMBER] Restraint on certain atoms during MD
Debarati DasGupta
(Wed Apr 22 2020 - 15:22:03 PDT)
6CF73A15FE1A4E99B37D565E1272ECC0.png
(7772 bytes)
Re: [AMBER] Restraint on certain atoms during MD
Debarati DasGupta
(Wed Apr 22 2020 - 15:10:04 PDT)
FD3FE68B931D4AB7931C5BF120EC2401.png
(67704 bytes)
[AMBER] Fwd: FATAL: allocation failure in ivector() error while running 3D-RISM calculations
Leena Aggarwal
(Thu Apr 23 2020 - 11:25:47 PDT)
script.sh
(143 bytes)
tleap.pdb
(286 bytes)
water.parm7
(8504 bytes)
04-23_18:48:45.png
(92503 bytes)
04-23_18:48:51.png
(103787 bytes)
[AMBER] wrong geometry amide nitrogen
Arnaud Bondon
(Fri Apr 24 2020 - 06:56:37 PDT)
NamidePyr.png
(67982 bytes)
[AMBER] minimizing a pyridine in water
Debarati DasGupta
(Sat Apr 25 2020 - 06:10:52 PDT)
27F9FCD505C24E35968C23E69DBC290B.png
(23149 bytes)
[AMBER] Ligand lose planarity
Jenny 148
(Sat Apr 25 2020 - 08:09:45 PDT)
nnnnn.PNG
(33314 bytes)
Re: [AMBER] minimizing a pyridine in water
Debarati DasGupta
(Sat Apr 25 2020 - 08:38:29 PDT)
3773FE3BF4C54F60BCB59D486053AC12.png
(7058 bytes)
7227E9CEB21B4408A03381096B88A082.png
(9499 bytes)
[AMBER] Recurring problem: Ligand lose planarity
Jenny 148
(Sat Apr 25 2020 - 21:49:45 PDT)
nnnnn.PNG
(33314 bytes)
Re: [AMBER] Interaction of cellulose-hemicellulose
Pinky Mazumder
(Sun Apr 26 2020 - 20:59:07 PDT)
li.PNG
(114911 bytes)
cell_hem_interaction.PNG
(81497 bytes)
[AMBER] AMBER leap issues constructing non-standard residue
Siddharth marwaha
(Mon Apr 27 2020 - 11:50:30 PDT)
A_smr_A.pdb
(4061 bytes)
A_smr_A.wa.pdb
(4570 bytes)
frcmod.smr
(3036 bytes)
leap.log
(38115 bytes)
LEAPY
(313 bytes)
SMR_RESIDUE.pdb
(4031 bytes)
smr.ac
(4447 bytes)
smr.prepin
(3048 bytes)
Re: [AMBER] minimizing a pyridine in water
Debarati DasGupta
(Mon Apr 27 2020 - 11:53:48 PDT)
3C68E36E6DE845A08FD0476A3C40D58F.png
(132501 bytes)
Re: [AMBER] wrong geometry amide nitrogen
Arnaud Bondon
(Wed Apr 29 2020 - 01:43:53 PDT)
data_testsirius4.rar
(33082 bytes)
Re: [AMBER] nativecontacts
Gustavo Seabra
(Wed Apr 29 2020 - 05:56:19 PDT)
bonds.awk
(2721 bytes)
Re: [AMBER] wrong geometry amide nitrogen
Junmei Wang
(Wed Apr 29 2020 - 07:12:46 PDT)
mytest.tar
(419840 bytes)
Re: [AMBER] wrong geometry amide nitrogen
Junmei Wang
(Wed Apr 29 2020 - 07:36:21 PDT)
mytest.tar.gz
(37897 bytes)
Re: [AMBER] wrong geometry amide nitrogen
Arnaud Bondon
(Thu Apr 30 2020 - 01:17:37 PDT)
bal2.pdb
(9148 bytes)
cR9.pdb
(25138 bytes)
PMB.pdb
(26385 bytes)
tat2.pdb
(24612 bytes)
PMB2.pdb
(26215 bytes)
Last message date
:
Thu Apr 30 2020 - 20:30:02 PDT
Archived on
: Mon Nov 04 2024 - 05:55:52 PST
358 messages
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