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 Fri Jul 19 2019 - 02:30:03 PDT
