Hi,
I have one more question considering center on the bilayer.
When I wrote commands:
autoimage
center ":PA | :PC | :OL" origin
and run cpptraj, I got following message:
ACTION SETUP FOR PARM 'step5_charmm2amber.parm7' (2 actions):
0: [autoimage]
Using first molecule as anchor.
127 molecules are fixed to anchor: 2 3 4 5 6 7 8 9 10 11 12 13 14
15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39
40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64
65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89
90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110
111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128
5010 molecules are mobile.
1: [center ":PA | :PC | :OL"]
Mask [:PA | :PC | :OL] corresponds to 0 atoms.
Warning: Mask contains 0 atoms.
Warning: Setup incomplete for [center]: Skipping
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:
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 - 01:30:02 PDT
