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Mikko Huhtala

  • Registered on: 04/16/2018
  • Last connection: 07/05/2018

Issues

Activity

07/05/2018

03:00 PM GROMACS Bug #2565 (Closed): gmx rms -skip does not skip
Using the -skip option in gmx rms seems to have no effect. The output .xvg file with the RMSD values has all frames l...

06/07/2018

01:02 PM GROMACS Bug #2480: pdb2gmx does not protonate correctly for united-atom Gromos
Work intervened, so I'm adding this comment late. I made another post weeks ago on the mailing list, and Justin Lemku...

05/10/2018

03:58 PM GROMACS Bug #2480: pdb2gmx does not protonate correctly for united-atom Gromos
That will work, but avoiding that was my whole point starting the thread on the mailing list. The manual entering of ...

05/09/2018

01:27 PM GROMACS Bug #2480: pdb2gmx does not protonate correctly for united-atom Gromos
Realized that the issue cuts both ways: renaming ASP to ASPH in the input will build a ASP topology, and having an ac...
12:04 PM GROMACS Bug #2480: pdb2gmx does not protonate correctly for united-atom Gromos
Tested 2018.1, the issue is still there.

04/16/2018

06:19 PM GROMACS Bug #2480 (New): pdb2gmx does not protonate correctly for united-atom Gromos
pdb2gmx builds ASPH residues without the HD2 hydrogen for Gromos 54a7. I changed manually the residue name of Asp95 i...

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