From: Douglas Houston (DouglasR.Houston_at_ed.ac.uk)
Date: Mon Feb 03 2014 - 03:52:42 CST
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
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.
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