Amber Archive Oct 2019 by messages with attachments
378 messages
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Starting
Mon Sep 30 2019 - 20:00:02 PDT,
Ending
Thu Oct 31 2019 - 06:00:02 PDT
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[AMBER] CPPTRAJ parameter file error
Rui Chen
(Tue Oct 01 2019 - 15:36:19 PDT)
10-01_at_3.47.01_PM.png
(98402 bytes)
10-01_at_3.45.59_PM.png
(135698 bytes)
[AMBER] ERROR: NaNs found in input coordinates.
HOCHEOL LIM
(Wed Oct 02 2019 - 17:13:05 PDT)
0.0.zip
(641772 bytes)
[AMBER] About STOP PMEMD Terminated Abnormally!
HOCHEOL LIM
(Sat Oct 05 2019 - 02:33:19 PDT)
heat.in
(658 bytes)
min.in
(291 bytes)
ti.in
(576 bytes)
[AMBER] tleap hangs when tries to read new residue
Dawid das
(Sun Oct 06 2019 - 10:09:05 PDT)
tleap.in
(152 bytes)
[AMBER] Force extension curve from ASMD
Aravind R
(Mon Oct 07 2019 - 00:27:12 PDT)
fig1.png
(143251 bytes)
Fig2.png
(226937 bytes)
Fig3.png
(274325 bytes)
[AMBER] could not find vdW (or other) parameters for type for virtually every amino acid atom
Dawid das
(Tue Oct 08 2019 - 09:03:59 PDT)
pack.zip
(545365 bytes)
Re: [AMBER] could not find vdW (or other) parameters for type for virtually every amino acid atom
Dawid das
(Tue Oct 08 2019 - 11:00:25 PDT)
leap.log
(726067 bytes)
Re: [AMBER] CPPTRAJ parameter file error
Rui Chen
(Wed Oct 09 2019 - 15:41:30 PDT)
10-09_at_4.19.01_PM.png
(194821 bytes)
[AMBER] tleap changes order of atoms in the parm file
Dawid das
(Thu Oct 10 2019 - 07:09:16 PDT)
tleap.in
(128 bytes)
[AMBER] PDB CONECT issues with OpenBabel 3.0 and antechamber
Miroslav Suruzhon
(Thu Oct 10 2019 - 08:41:57 PDT)
Files.zip
(5870 bytes)
Re: [AMBER] Adding OH- to a water box
Lucas Bandeira
(Sun Oct 13 2019 - 10:50:48 PDT)
tleap.out
(14901 bytes)
oh.pdb
(158 bytes)
tleap.in
(274 bytes)
interfaceNaOH.pdb
(284835 bytes)
na.pbd
(79 bytes)
[AMBER] Problem in extracting pdb file from mdcrd file
Airy Sanjeev
(Mon Oct 14 2019 - 01:07:15 PDT)
analysis.input
(102 bytes)
Re: [AMBER] Thermodynamic integration
Sadaf Rani
(Mon Oct 14 2019 - 03:59:22 PDT)
min.out
(26955 bytes)
[AMBER] PTRAJ (clustering)-Segmentation fault
Rui Chen
(Tue Oct 15 2019 - 08:35:56 PDT)
244898.out
(3842 bytes)
Re: [AMBER] minimize protein with a small molecule tethered at a fixed location
Debarati DasGupta
(Wed Oct 16 2019 - 06:32:02 PDT)
minimized.pdb
(371033 bytes)
setup_ABL_Kinase_transformed.pdb
(374286 bytes)
tleap.in
(445 bytes)
Re: [AMBER] make install errors
Alen Ahmetovic
(Wed Oct 16 2019 - 15:34:49 PDT)
amberinstall.txt
(576174 bytes)
[AMBER] sander/lmod parallel execution
Charles-Alexandre Mattelaer
(Mon Oct 21 2019 - 07:07:29 PDT)
Run.lmod
(1220 bytes)
[AMBER] Error adding OH⁻ ions in a simulation box
Lucas Bandeira
(Mon Oct 21 2019 - 13:44:54 PDT)
frcmod.oh
(67 bytes)
naAmber.pdb
(85 bytes)
ohAmber.pdb
(166 bytes)
ohAmber.mol2
(363 bytes)
tleap.in
(389 bytes)
tleap.out
(12596 bytes)
Re: [AMBER] sander/lmod parallel execution
Charles-Alexandre Mattelaer
(Tue Oct 22 2019 - 00:39:09 PDT)
2k71.inpcrd
(9282 bytes)
Run.lmod
(1325 bytes)
2k71.prmtop
(127373 bytes)
10-22_09-37-13.png
(91565 bytes)
[AMBER] compiling Amber with gcc 9.2 and intel mpi 2019
Vlad Cojocaru
(Mon Oct 28 2019 - 07:57:51 PDT)
make_mpi.log
(617742 bytes)
Last message date
:
Thu Oct 31 2019 - 06:00:02 PDT
Archived on
: Mon Dec 09 2024 - 05:55:49 PST
378 messages
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