VMD-L Mailing List

From: Udit Aswal (udit0000_at_gmail.com)
Date: Fri Mar 31 2017 - 01:37:54 CDT

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
Udit