Brian & Pawel,
Thanks for the information. I have done a simulation with a truncated
octahedron in the past in NAMD using AMBER .prmtop/.inpcrd, but that case
was easier due to solvateOct LeAP command.
This time I create a protein-membrane-water system as a hexagona prism with
CHARMM-GUI, I modified the file as described in the tutorial and passed it
to LeAP. There I did:
Regarding the last line of .inpcrd, it seem that VMD perceives the lattice
vector angles differently. According to this post:
http://archive.ambermd.org/200907/0035.html
the last .inpcrd line correspond to "a b c alpha beta gamma". However, VMD
definition of alpha, beta and gamma is not exactly as in AMBER. See the
example below which shows the impact of NPT equilibration with NAMD were
the protein was constrained:
## last .inpcrd line: 106.0000000 106.0000000 86.0000000 90.0000000
90.0000000 120.000000
# box info at the beginning:
% molinfo top get {a b c}
106.000000 106.000008 87.000000
% molinfo top get {alpha beta gamma}
90.000000 90.000000 60.000004
# box info at the end:
% molinfo top get {a b c}
97.726463 98.022034 76.186539
% molinfo top get {alpha beta gamma}
90.000000 90.000000 60.099697
## last .inpcrd line: 106.0000000 106.0000000 86.0000000 60.0000000
90.0000000 90.000000
# box info at the beginning:
% molinfo top get {a b c}
106.000000 106.000008 87.000000
% molinfo top get {alpha beta gamma}
90.000000 90.000000 60.000004
# box info at the end:
% molinfo top get {a b c}
95.999474 95.565758 79.677513
% molinfo top get {alpha beta gamma}
90.000000 90.000000 59.849758
As I can judge from the above results, "106.0000000 106.0000000
86.0000000 90.0000000 90.0000000 120.000000" is equivalent to
"106.0000000 106.0000000 86.0000000 60.0000000 90.0000000 90.000000",
namely both Pawel and
http://ambermd.org/namd/namd_amber.html are correct.
On 9 November 2013 00:03, Pawel <pawelrc.gmail.com> wrote:
> Hi Thomas,
>
> Just to add to what Brian said, you can use AmberTool's AddToBox
> program to create a hexagonal unit cell. Just make sure you specify
> coordinates consistent with a hexagonal space group (a a c 90 90 120).
> You can then also use PropPDB if you wish to create a model of several
> hexagonal unit cells side by side (for a lipid membrane, just extend
> them out in a and b not c directions). You can then simulate it in Amber
> if you'd like which will treat this just like a triclinic cell (of which
> a hexagonal cell is a special case). For NAMD, take a look at:
>
> http://ambermd.org/namd/namd_amber.html
>
> Section 4 details how to properly set the cellBasisVectors in NAMD
> (although I think there is an error. If I'm not mistaken, the bottom
> line of your crd/rst file should read
>
> d d h 90.0 90.0 120.0
>
> not
>
> d d h 60.0 90.0 90.0
>
> At least that's how it's worked for me in the past. Also take note of
> the other information on that page. There's some intricacy to using
> Amber in NAMD.
>
> Pawel
>
>
>
> On 11/08/2013 09:32 AM, Brian Radak wrote:
> > I'm not an expert on non-orthorhombic boxes, but I did once get AMBER to
> > work correctly with a rhombic dodecahedron. The solution was to:
> >
> > 1) read a pdb of the water box into leap
> > 2) use "setBox" to set dummy box information
> > 3) edit the box vectors in the inpcrd by hand
> > 4) edit IFBOX to be equal to 3 by hand in the prmtop
> >
> > I checked all of this by using the "image familiar" command in
> > ptraj/cpptraj. However, be aware that AMBER will simulate in the
> triclinic
> > representation, which will make it quite difficult to visualize what is
> > actually going on. No guarantees on that working for sure though.
> >
> > Regards,
> > Brian
> >
> >
> > On Thu, Nov 7, 2013 at 7:37 PM, Thomas Evangelidis <tevang3.gmail.com
> >wrote:
> >
> >> Dear list,
> >>
> >> Does anyone know if I can create a hexagonal membrane patch with
> lipid11 ff
> >> to run a simulation in a hexagonal unit cell with NAMD? CHARMM-GUI
> provides
> >> an option to create a hexagonal box but I think in the .prmtop file
> there
> >> is a pointer named "IFBOX" which determines the box size, and since
> AMBER
> >> does not support that kind of shape I suspect there might be a conflict
> >> with the cell basis vectors in the NAMD configuration file. The same may
> >> apply with the lattice vectors written in the last line of .inpcrd.
> >>
> >> Other than that, the lipid11 tutorial states that I should choose a
> >> Rectangular box type in CHARMM-GUI since this geometry is required for
> >> constant surface tension. Will there be a problem if I choose a
> Hexagonal
> >> box type and run the simulation in NAMD provided that I define correctly
> >> the cell basis vectors?
> >>
> >> Could anyone please clarify these points?
> >>
> >> thanks,
> >> Thomas
> >>
> >>
> >>
> >> --
> >>
> >> ======================================================================
> >>
> >> Thomas Evangelidis
> >>
> >> PhD student
> >> University of Athens
> >> Faculty of Pharmacy
> >> Department of Pharmaceutical Chemistry
> >> Panepistimioupoli-Zografou
> >> 157 71 Athens
> >> GREECE
> >>
> >> email: tevang.pharm.uoa.gr
> >>
> >> tevang3.gmail.com
> >>
> >>
> >> website: https://sites.google.com/site/thomasevangelidishomepage/
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
>
> _______________________________________________
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>
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Tue Nov 12 2013 - 04:30:03 PST
