Hi Sally,
I have experienced very similar problems in the past. What I've found works
best is something a little different than what has been suggested so far. I
typically do the following:
center mass origin '.1-4185 & .C114,C214,C314,C412,C514,C614'
image center origin familiar
Where atoms 1-4185 correspond to the top leaflet of the bilayer, and C114,
C214, C314, etc are the atom names of the terminal carbon in each acyl
chain of the lipids. In most cases, this has the effect of centering the
bilayer at the origin, or at least very very close. I've found it works
best to specify only one leaflet, because cpptraj has the tendency to still
place the water in the middle if you specify the whole leaflet or all of
the terminal carbons (especially for more complex bilayers).
Hope this helps!
- Amy
On Thu, Jul 7, 2016 at 10:43 AM, Dickson, Callum J <
callum.dickson09.imperial.ac.uk> wrote:
> Another option you could try is:
>
>
> center mass origin :1-384
> image center origin familiar
>
>
> Where you should alter the :1-384 mask so that it covers all of the lipid
> residues in your bilayer.
>
>
> Best,
>
> Callum
>
> ________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Sent: Thursday, July 7, 2016 10:37:57 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] re-imaging bilayer
>
> Hi,
>
> On Thu, Jul 7, 2016 at 7:41 AM, Sally Pias <sallypias.gmail.com> wrote:
> >
> > "Autoimage" does a great job but splits the water unevenly on the two
> sides
> > of the bilayer, leaving a very thin water layer on one side. It does so
>
> What if after you 'autoimage', you then re-center the bilayer (with
> 'center') and then 'image' *only* the water?
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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--
Amy Rice
Ph.D. Student
Physics Department
Illinois Institute of Technology
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Received on Thu Jul 07 2016 - 09:30:03 PDT
