VMD-L Mailing List

From: Udit Aswal (udit0000_at_gmail.com)
Date: Fri Mar 31 2017 - 06:49:36 CDT

Dear Ramon,
Thanks! That was really helpful.
I need one more favor to ask,i.e., if you could tell me if there is any way
to do the "vicinity check" of only tail atoms of a lipid molecule?

Regards
Udit

On Fri, Mar 31, 2017 at 3:35 PM, Ramon Guixà <ramonguixxa_at_gmail.com> wrote:

> Hi Udit, I actually misunderstood your question.
>
> You might have lipid and protein molecules with the same resid 40. Try: "name
> P and same residue as within 5 of protein and *resid *40" or "name P and
> same residue as within 5 of *residue *40"
>
> Btw, if you wanna test visually, better go for the same selection you are
> using to measure the distance, namely "name P and same residue as within
> 5 of name HD23 and *residue *40"
>
> Hope that helps,
> Ramon
>
>
> On Fri, Mar 31, 2017 at 11:32 AM, Udit Aswal <udit0000_at_gmail.com> wrote:
>
>> Dear Ramon,
>> "exwithin" still shows the same result. I am attaching the screenshot of
>> it with the distance shown.
>>
>> Regards
>> Udit
>>
>>
>>
>> [image: Inline image 2][image: Inline image 4]
>>
>> On Fri, Mar 31, 2017 at 1:44 PM, Ramon Guixà <ramonguixxa_at_gmail.com>
>> wrote:
>>
>>> Hi Udit, using 'exwithin' instead of 'within' should do the trick.
>>>
>>> Ramon
>>>
>>>
>>>
>>> On 31 Mar 2017 09:26, "Udit Aswal" <udit0000_at_gmail.com> wrote:
>>>
>>> Hello,
>>> I am trying to do vicinity analysis of phosphorus atoms(present in a
>>> DPPC molecule head group) around any specific residue.
>>> The problem I am facing is that instead of looking for only phosphorus
>>> atoms, if, within that vicinity there is any other atom of the same DPPC
>>> residue, then it also 'counts it' as the phosphorus atom of the same DPPC
>>> residue even if that P atom is not within the vicinity.
>>> It would be really helpful if someone could tell me the way to fix this--94eb2c12f94c6cd4c1054c056742--
--94eb2c12f94c6cd4c3054c056743--