From: Douglas Houston (DouglasR.Houston_at_ed.ac.uk)
Date: Wed Jan 22 2014 - 08:31:03 CST
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):
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
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
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.
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?
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
> 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.
> 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.
Dr. Douglas R. Houston
Institute of Structural and Molecular Biology
Michael Swann Building
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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