VMD-L Mailing List

From: Ramon Guixà (ramonguixxa_at_gmail.com)
Date: Fri Mar 31 2017 - 05:05:50 CDT

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.
>>
>> The command i am giving is-
>> "name P and same residue as (within 5 of resid 40)"
>>
>>
>> Regards
>>
>>
>>
>


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