Amber Archive Jan 2023 by messages with attachments

138 messages: Starting Sun Jan 01 2023 - 19:00:03 PST, Ending Tue Jan 31 2023 - 12:30:03 PST
This period: Most recent messages
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Re: [AMBER] error with titration curve in Constant pH tutorial Vaibhav Dixit via AMBER (Mon Jan 02 2023 - 01:24:56 PST)
1. graph.png (113991 bytes)
[AMBER] Non-standard KCX residue with missing hydrogen on carbamate and charge -1 Barbara Herlah via AMBER (Wed Jan 04 2023 - 21:35:33 PST)
1. Inline_image_OWAPstImg969435ecb07e49-a105-4870-83cd-c8593fec4580.png (52487 bytes)
2. Inline_image_OWAPstImg263658efbcd7ce-0bb7-429f-b4a0-52403cb6e8ce.png (169481 bytes)
3. Inline_image_OWAPstImg604716642bb317-4448-49cb-affd-52a9925ef4e6.png (38927 bytes)
4. leap1.log (19268 bytes)
[AMBER] Thermodynamic integration for charge-changing mutations Skanda Sastry via AMBER (Thu Jan 05 2023 - 17:22:18 PST)
1. equil.in (1526 bytes)
2. equilnorest.in (1397 bytes)
3. submission.sh (777 bytes)
4. min.in (836 bytes)
5. heat.in (1568 bytes)
[AMBER] amber 22 installation on ubuntu 18 Dulal Mondal via AMBER (Sat Jan 07 2023 - 06:54:18 PST)
1. 01-07_19-08-36.diff (9546 bytes)
2. 01-07_19-08-36.log (253064 bytes)
3. 01-07_19-47-13.log (49672 bytes)
4. 01-07_19-47-13.diff (21674 bytes)
[AMBER] no decomposition output for amber22 MMGBSA Adam Jarmula via AMBER (Wed Jan 11 2023 - 12:24:29 PST)
1. E81A_NOH_A_c0_300ns_mmgbsa_decomp.dat (93 bytes)
[AMBER] Question concerning the GLYCAM force field Jiang, Yaoyukun via AMBER (Mon Jan 16 2023 - 19:48:35 PST)
1. image001.png (211332 bytes)
2. oligosaccharide.png (243328 bytes)
3. Lig2.pdb (4536 bytes)
Re: [AMBER] Issues with nucleic acid simulations Prithviraj Nandigrami via AMBER (Fri Jan 20 2023 - 12:47:03 PST)
1. input_file.pdb (144886 bytes)
[AMBER] tleap parameter file Mac Kevin Braza via AMBER (Fri Jan 20 2023 - 13:52:00 PST)
1. protein.pdb (423091 bytes)
[AMBER] Problem met in running GBn2 model Jiaan Zhu via AMBER (Sun Jan 22 2023 - 03:32:37 PST)
1. Phosphate_aggregation.png (340578 bytes)
2. dna.prmtop (122032 bytes)
3. dna.rst7 (9511 bytes)
4. min.in (159 bytes)
5. equ.in (1085 bytes)
[AMBER] Segmentation fault when trying outputting MBAR data in vacuum Miroslav Suruzhon via AMBER (Wed Jan 25 2023 - 09:24:13 PST)
1. Inputs.zip (3797 bytes)
[AMBER] idecomp = 1 for TI simulations: Energies not printed / cannot be calculated He, Amy via AMBER (Fri Jan 27 2023 - 15:14:06 PST)
1. prd0.in (487 bytes)
2. prd.group (270 bytes)
3. prd0.out (9270 bytes)
Re: [AMBER] Random failure of parmchk2? Brian Radak via AMBER (Mon Jan 30 2023 - 08:23:17 PST)
1. parmchk_mwe.sh (5717 bytes)