Amber Archive Oct 2019 by messages with attachments

[AMBER] CPPTRAJ parameter file error Rui Chen (Tue Oct 01 2019 - 15:36:19 PDT)
1. 10-01_at_3.47.01_PM.png (98402 bytes)
2. 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)
1. 0.0.zip (641772 bytes)
[AMBER] About STOP PMEMD Terminated Abnormally! HOCHEOL LIM (Sat Oct 05 2019 - 02:33:19 PDT)
1. heat.in (658 bytes)
2. min.in (291 bytes)
3. ti.in (576 bytes)
[AMBER] tleap hangs when tries to read new residue Dawid das (Sun Oct 06 2019 - 10:09:05 PDT)
1. tleap.in (152 bytes)
[AMBER] Force extension curve from ASMD Aravind R (Mon Oct 07 2019 - 00:27:12 PDT)
1. fig1.png (143251 bytes)
2. Fig2.png (226937 bytes)
3. 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)
1. 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)
1. leap.log (726067 bytes)
Re: [AMBER] CPPTRAJ parameter file error Rui Chen (Wed Oct 09 2019 - 15:41:30 PDT)
1. 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)
1. tleap.in (128 bytes)
[AMBER] PDB CONECT issues with OpenBabel 3.0 and antechamber Miroslav Suruzhon (Thu Oct 10 2019 - 08:41:57 PDT)
1. Files.zip (5870 bytes)
Re: [AMBER] Adding OH- to a water box Lucas Bandeira (Sun Oct 13 2019 - 10:50:48 PDT)
1. tleap.out (14901 bytes)
2. oh.pdb (158 bytes)
3. tleap.in (274 bytes)
4. interfaceNaOH.pdb (284835 bytes)
5. na.pbd (79 bytes)
[AMBER] Problem in extracting pdb file from mdcrd file Airy Sanjeev (Mon Oct 14 2019 - 01:07:15 PDT)
1. analysis.input (102 bytes)
Re: [AMBER] Thermodynamic integration Sadaf Rani (Mon Oct 14 2019 - 03:59:22 PDT)
1. min.out (26955 bytes)
[AMBER] PTRAJ (clustering)-Segmentation fault Rui Chen (Tue Oct 15 2019 - 08:35:56 PDT)
1. 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)
1. minimized.pdb (371033 bytes)
2. setup_ABL_Kinase_transformed.pdb (374286 bytes)
3. tleap.in (445 bytes)
Re: [AMBER] make install errors Alen Ahmetovic (Wed Oct 16 2019 - 15:34:49 PDT)
1. amberinstall.txt (576174 bytes)
[AMBER] sander/lmod parallel execution Charles-Alexandre Mattelaer (Mon Oct 21 2019 - 07:07:29 PDT)
1. Run.lmod (1220 bytes)
[AMBER] Error adding OH⁻ ions in a simulation box Lucas Bandeira (Mon Oct 21 2019 - 13:44:54 PDT)
1. frcmod.oh (67 bytes)
2. naAmber.pdb (85 bytes)
3. ohAmber.pdb (166 bytes)
4. ohAmber.mol2 (363 bytes)
5. tleap.in (389 bytes)
6. tleap.out (12596 bytes)
Re: [AMBER] sander/lmod parallel execution Charles-Alexandre Mattelaer (Tue Oct 22 2019 - 00:39:09 PDT)
1. 2k71.inpcrd (9282 bytes)
2. Run.lmod (1325 bytes)
3. 2k71.prmtop (127373 bytes)
4. 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)
1. make_mpi.log (617742 bytes)

Last message date: Thu Oct 31 2019 - 06:00:02 PDT
Archived on: Wed Dec 25 2024 - 05:55:53 PST

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