Thank you so much, now everything looks good!
Maria
pt., 19 lip 2019 o 14:10 Daniel Roe <daniel.r.roe.gmail.com> napisał(a):
> After you ‘center’ you need to reimage the water and ions only back into
> the primary unit cell via the ‘image’ command, e.g.:
>
> image :TIP3,SOD
>
> Modify the mask as appropriate if you have other ions etc.
>
> Hope this helps,
>
> -Dan
>
> On Fri, Jul 19, 2019 at 1:35 PM Maria Bzówka <m.bzowka.tunnelinggroup.pl>
> wrote:
>
> > Indeed, the mask is ':POPC', but I still have some doubts when I
> visualize
> > it in VMD (you can see in the attached file how it looks with the pbc
> box)
> >
> > cpptraj commands:
> > autoimage
> > center ":POPC"
> >
> > Maria
> >
> >
> > pt., 19 lip 2019 o 11:13 Daniel Roe <daniel.r.roe.gmail.com> napisał(a):
> >
> > > Hi,
> > >
> > > On Fri, Jul 19, 2019 at 4:17 AM Maria Bzówka <
> m.bzowka.tunnelinggroup.pl
> > >
> > > wrote:
> > > > I assume that this is caused by the fact that CHARMM-GUI (which was
> > used
> > > to
> > > > build the membrane) does not split the lipid into three "residues".
> > > > However, when I tried to use other mask definitions e.g. "POPC" or
> > > "MEMB" i
> > > > got the error:
> > >
> > > If you are using CHARMM membrane parameters, I suspect the mask you
> > > need is ':POPC'. Cpptraj actually has some useful commands you can use
> > > to figure out what things are named in a given topology file/test mask
> > > expressions; 'molinfo short', 'resinfo', 'atoms', etc. For example,
> > > below I will paste the output from cpptraj (run interactively) on a
> > > loaded PSF containing some proteins embedded in a lipid bilayer:
> > >
> > > > molinfo short
> > > [molinfo short]
> > > #Mol Count Natom Nres
> > > PHE 28 376 22
> > > POPC 525 134 1
> > > POPG 175 127 1
> > > TIP3 5950 3 1
> > > SOD 63 1 1
> > > > resinfo ^29
> > > [resinfo ^29]
> > > #Res Name First Last Natom #Orig #Mol
> > > 617 POPC 10529 10662 134 1 29
> > >
> > > So in this case, if I wanted to select the entire membrane I would use
> > > ':POPC,POPG' (or alternatively ':POP?').
> > >
> > > Hope this helps,
> > >
> > > -Dan
> > >
> > > >
> > > > AUTOIMAGE: To box center based on center of mass, anchor is first
> > > molecule.
> > > > [center "MEMB" origin]
> > > > CENTER: Centering coordinates using geometric center of atoms in
> > mask
> > > > (*) to
> > > > coordinate origin.
> > > > Error: [center] Not all arguments handled: [ MEMB ]
> > > > 1 errors encountered reading input.
> > > >
> > > > So here my question is, how to define a mask properly so that it
> covers
> > > the
> > > > entire bilayer?
> > > >
> > > > Thank you in advance
> > > >
> > > > Maria
> > > >
> > > >
> > > >
> > > >
> > > > pon., 15 lip 2019 o 16:39 Daniel Roe <daniel.r.roe.gmail.com>
> > > napisał(a):
> > > >
> > > > > Hi,
> > > > >
> > > > > This is happening because autoimage is choosing a single molecule
> > from
> > > > > one of the bilayers as the anchor. After "autoimage", you could
> > > > > 'center' on the bilayer (i.e. use 'center' and select the entire
> > > > > bilayer) and then image only water, ions with 'image bymol
> > > > > :WAT,Na+,Cl-' etc.
> > > > >
> > > > > Alternatively you could try to choose the end of one of the lipid
> > > > > chains (near the bilayer center) as the anchor instead of an entire
> > > > > lipid.
> > > > >
> > > > > Hope this helps,
> > > > >
> > > > > -Dan
> > > > >
> > > > > On Mon, Jul 15, 2019 at 9:53 AM Maria Bzówka <
> > > m.bzowka.tunnelinggroup.pl>
> > > > > wrote:
> > > > > >
> > > > > > Hi Dan,
> > > > > >
> > > > > > Thank you for your suggestion, it works. However, the new problem
> > > showed
> > > > > > up. Right now, the water layers do not have the same thickness
> > (you
> > > can
> > > > > > see in the attached file). I don't know what to think about it.
> > > Does it
> > > > > > mean that something is wrong with the equilibration itself?
> > > > > >
> > > > > > Maria
> > > > > >
> > > > > > pon., 15 lip 2019 o 15:26 Daniel Roe <daniel.r.roe.gmail.com>
> > > > > napisał(a):
> > > > > >
> > > > > > > Hi,
> > > > > > >
> > > > > > > 'autoimage origin' will center the system at the coordinate
> > origin
> > > > > > > (bottom corner of the box). Just omit the 'origin' keyword from
> > the
> > > > > > > autoimage command and remove the subsequent center/image
> > commands.
> > > > > > >
> > > > > > > Hope this helps,
> > > > > > >
> > > > > > > -Dan
> > > > > > >
> > > > > > > On Mon, Jul 15, 2019 at 7:32 AM Maria Bzówka <
> > > > > m.bzowka.tunnelinggroup.pl>
> > > > > > > wrote:
> > > > > > > >
> > > > > > > > Hi all,
> > > > > > > >
> > > > > > > > I work with the system which consists of 128 lipids bilayer
> and
> > > water
> > > > > > > > molecules. I used the cpptraj to center the whole system
> using
> > > > > following
> > > > > > > > commands:
> > > > > > > >
> > > > > > > > trajin step6.1_equilibration.nc
> > > > > > > > trajin step6.2_equilibration.nc
> > > > > > > > trajin step6.3_equilibration.nc
> > > > > > > > trajin step6.4_equilibration.nc
> > > > > > > > trajin step6.5_equilibration.nc
> > > > > > > > trajin step6.6_equilibration.nc
> > > > > > > > autoimage origin
> > > > > > > > center :1-128 mass origin
> > > > > > > > image origin center familiar
> > > > > > > >
> > > > > > > > In VMD the system itself looks fine, but when I wanted to
> check
> > > the
> > > > > pbc
> > > > > > > > box, it only partially overlaps with the system (you can see
> in
> > > the
> > > > > > > > attached file).
> > > > > > > > Should I somehow change the cpptraj commands?
> > > > > > > >
> > > > > > > > Thank you in advance for suggestions
> > > > > > > >
> > > > > > > > Maria
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Received on Mon Jul 22 2019 - 00:30:02 PDT
