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

[SHAHEE ISLAM]

i am doing this simulation with martini coarse grained force field. so i
just replace p and n by bead name and it is working now.
thank you so much again for your reply.

On Wed, Oct 30, 2019 at 1:04 PM SHAHEE ISLAM <islamshahee at gmail.com> wrote:

> 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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>>
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