From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Feb 03 2014 - 04:34:48 CST
Well, in VMD using charmm format, there's a solvate plugin as you found
already and an ionize plugin aswell. You might be interested in checking the
manual of "psfgen" itself.
> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Douglas Houston
> Gesendet: Montag, 3. Februar 2014 10:53
> An: namd-l_at_ks.uiuc.edu
> Betreff: namd-l: Re: Various questions
> And now I've found that the Solvate VMD plugin can automatically
> detect the box size (question 2).
> This leads to a fresh question however. How do I add ions as well as
> water? The tutorial mentions ions should be added to neutralise the
> system but neglects to say how. I can also find no mention of adding
> ions in what Solvate documentation I can find (i.e. its webpage).
> Quoting Douglas Houston <DouglasR.Houston_at_ed.ac.uk> on Wed, 22 Jan
> 2014 14:31:03 +0000:
> > I think I've made some headway in answering question 6. The
> > following I found in the CHARMM parameter file
> > (par_all27_prot_lipid.inp):
> > BONDS
> > HA CT2 309.000 1.1110 ! ALLOW ALI - from a.a. side chains
> > CTL2 HAL2 309.00 1.111 ! alkanes, 4/98 - from e.g. hexene
> > ANGLES
> > HA CT2 CT2 26.500 110.10 22.53 2.17900 ! ALLOW ALI -
> > from a.a. side chains
> > HAL2 CTL2 CTL2 26.500 110.10 22.53 2.179 ! alkane, 4/98 -
> > from e.g. hexene
> > DIHEDRALS
> > X CT2 CT2 X 0.1950 3 0.00 ! ALLOW ALI - from
> > a.a. side chains (no HA CT2 CT2 HA dihedral specified)
> > CT2 CT2 CT2 CT2 0.1500 1 0.00 ! ALLOW ALI - from a.a.
> > side chains
> > X CTL2 CTL2 X 0.1900 3 0.00 ! alkane, 4/98, yin and
> > mackerell - from e.g. hexene (no HAL2 CTL2 CTL2 HAL2 dihedral
> > specified)
> > CTL2 CTL2 CTL2 CTL2 0.10 2 180.00 ! alkane, 4/98, adm jr. -
> > from e.g. hexene
> > CTL2 CTL2 CTL2 CTL2 0.15 4 0.00 ! alkane, 4/98, adm jr. -
> > from e.g. hexene
> > CTL2 CTL2 CTL2 CTL2 0.10 6 180.00 ! alkane, 4/98, adm jr. -
> > from e.g. hexene
> > Bonds and angles are identical but I'm trying to understand the
> > dihedral entries. First, there doesn't appear to be a specific
> > dihedral for amino acid side chain or lipid H-CH2-CH2-H so
> > presumably the X-C-C-X entries get used (please correct me if I'm
> > wrong). Then there are 3 entries for the "lipid" CH2-CH2-CH2-CH2
> > dihedral and only one for the "side chain". Which of the 3 "lipid"
> > dihedrals get used in any given situation? Also, shouldn't the
> > periodicities be 1 or 3, what does it mean that the "lipid" entries
> > have 2, 4 and 6?
> > cheers,
> > Doug
> > Quoting Douglas Houston <DouglasR.Houston_at_ed.ac.uk> on Tue, 21 Jan
> > 2014 15:42:14 +0000:
> >> Dear all,
> >> I am a beginner when it comes to NAMD but have been working through
> >> the helpful tutorials. However, I have a few questions that I have
> >> not been able to find the answers to:
> >> 1. The NAMD tutorial includes an example of a simulation in a
> >> sphere with non-periodic boundary conditions. Why do I only ever
> >> read about simulating in a box with periodic boundary conditions in
> >> the literature? Maybe I'm just not reading enough ;-) but is there
> >> a discussion of the pros and cons of each anywhere?
> >> 2. I have used mainly Gromacs in the past - Gromacs automatically
> >> detects and applies its equivalents of NAMD's Cellorigin and
> >> BasisVector 1, 2 and 3 keywords. Is there a way to get NAMD to do
> >> this?
> >> 3. From the NAMD tutorial: "One typically minimizes the system and
> >> then equilibrates with the atoms in the protein fixed in space."
> >> But there is no mention of this in the example .conf file that is
> >> provided. What are the keywords relevant for fixing solute? Does
> >> anyone have an example .conf file of a "standard" protein
> >> relaxation protocol? I have seen example protocols for Gromacs and
> >> Desmond but is there a "default" one for NAMD?
> >> 4. I have been working on generating a .psf for an olefin stapled
> >> peptide. I have added an entry to the CHARMM parameter file and got
> >> psfgen to output a .psf that looks OK in VMD (by OK I mean that the
> >> right bonds are visible and hydrogen addition looks sensible).
> >> However, I'm worried there may be some BOND, DIHE, IMPR or other
> >> inappropriate descriptions I've missed (for example, I've used
> >> patches to connect the linker to the backbone, which necessitated
> >> deleting the existing backbone peptide bonds - but have I deleted
> >> everything I should have?). I understand a validation run might
> >> identify incorrect atomic motions but before that is there a way to
> >> visualise all entries in the .psf file using VMD (or should I
> >> direct this to the VMD mailing list)?
> >> 5. Related to 4., are entries like IMPR disregarded if there is not
> >> a corresponding BOND? If so that would make me less worried about
> >> catching every single one.
> >> 6. Why are the hexene methanediyl hydrogens in the
> >> top_all27_prot_lipid.inp file a different atom type (HAL2) than
> >> e.g. lysine side chain methanediyl hydrogens (i.e. HA)? I note the
> >> charges are the same. The olefin staple is essentially a
> >> monounsaturated lipid and I've built it using -CH2 parameters taken
> >> from amino acid side chains but the hexene parameters seem equally
> >> correct to me. What's the difference between these atom types?
> >> 7. I think that's enough questions for now!
> >> Many thanks for any advice.
> >> cheers,
> >> Doug
> >> _____________________________________________________
> >> Dr. Douglas R. Houston
> >> Lecturer
> >> Room 3.23
> >> Institute of Structural and Molecular Biology
> >> Michael Swann Building
> >> King's Buildings
> >> University of Edinburgh
> >> Edinburgh, EH9 3JR, UK
> >> Tel. 0131 650 7358
> >> --
> >> The University of Edinburgh is a charitable body, registered in
> >> Scotland, with registration number SC005336.
> > _____________________________________________________
> > Dr. Douglas R. Houston
> > Lecturer
> > Room 3.23
> > Institute of Structural and Molecular Biology
> > Michael Swann Building
> > King's Buildings
> > University of Edinburgh
> > Edinburgh, EH9 3JR, UK
> > Tel. 0131 650 7358
> > --
> > The University of Edinburgh is a charitable body, registered in
> > Scotland, with registration number SC005336.
> Dr. Douglas R. Houston
> Room 3.23
> Institute of Structural and Molecular Biology
> Michael Swann Building
> King's Buildings
> University of Edinburgh
> Edinburgh, EH9 3JR, UK
> Tel. 0131 650 7358
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
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