[gmx-users] how to select head groups of lipid within 10 angstrom of protein

[SHAHEE ISLAM]

i am so sorry for the late reply. I have applied both of your suggestion
but still it does not working.
syntax error
invalid selection 'POPG and name P* N* within 1.0 of Protein'
can you please guide me to solve the error.

On Fri, Oct 25, 2019 at 3:39 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/25/19 5:38 AM, Peter Stern wrote:
> > You are probably causing your command to run in the background with
> “&”.  Try using “and” instead.
>
> In addition to this, the selection string needs to be enclosed by single
> quotes.
>
> -Justin
>
> > Peter
> >
> > Sent from my iPhone
> >
> >> On Oct 25, 2019, at 11:45 AM, SHAHEE ISLAM <islamshahee at gmail.com>
> wrote:
> >>
> >> Hi,
> >> I am trying to calculate the angle between P and N vector of my lipid
> >> (popc+popg) with regards to the z axis to see how the protein is
> affecting
> >> the membrane. I am using this command, but it does not working
> >> gmx select -f *.xtc -s *.tpr -select POPG & name P* N* within 1.0 of
> >> Protein -oi number.dat
> >> but the problem is, when the command is running only
> >>   gmx select -f *.xtc -s *.tpr -select POPG
> >> this command.
> >> Can anyone please guide me what i am doing wrong.
> >> Thanking you
> >> Shahee
> >> --
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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
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