VMD-L Mailing List

From: Ramon Guixà (ramonguixxa_at_gmail.com)
Date: Fri Mar 31 2017 - 09:06:56 CDT

Hey,

Well, this really depends on the naming scheme of the force field you are
using. When selecting part of molecules wildcards come anyway really handy,
for example:

Selecting lipid tails in Charmm POPC molecules: "resname POPC and name
"C[23].*" and not name "C[123]"

But as I said, you will have to fine tune the command for your particular
topology.

A couple of advices:
- Just in case you don't know , the fast radial distribution function
implemented in vmd (http://www.ks.uiuc.edu/Research/vmd/plugins/gofrgui/)
is a powerful tool to inspect the vicinity of an atom or selection.
- On the other hand, the membplugin for vmd contains several
functionalities to compute membrane/lipid properties and lipid-protein
interactions. Is not a buil-in plugin though, you can download and install
from: https://sourceforge.net/projects/membplugin/

Hope this helps,
Ramon

On Fri, Mar 31, 2017 at 1:49 PM, Udit Aswal <udit0000_at_gmail.com> wrote:

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


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