Re: AW: Re: Various questions

From: Douglas Houston (DouglasR.Houston_at_ed.ac.uk)
Date: Tue Feb 04 2014 - 07:26:05 CST

Hi Norman,

Many thanks for your reply, the Ionize plugin looks ideal.

I think I spoke too soon when I said that the Solvate plugin solved
question 2 - yes it detects the boxsize but it doesn't output the
dimensions for use in NAMD. Therefore I wrote a little script to do
that to ease the NAMD configuration file creation (attached - the
first line should point to your Korn shell exe).

Interestingly the CellOrigin values the script outputs differ slightly
from the "measure center" VMD TkCon function (which outputs
inexplicably large numbers of significant figures) - I'm not sure what
the source of the difference is but both seem to work.

cheers,

Doug

Quoting Norman Geist <norman.geist_at_uni-greifswald.de> on Mon, 3 Feb
2014 11:34:48 +0100:

> 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.
>
> Norman Geist.
>
>
>> -----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
>> 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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