[gmx-users] Calculate probability of presence of water around a residues

[pooja kesari]

Dear Users,
I have two queries

1. I have tried using the select command to Calculate probability of
presence of water around a residues by creating an a group in my index
analyze.ndx contains a group named ser76 which has the atom position near
which i want to find this water (say atom 1313)

*gmx select -s md_0_1.tpr -f md_0_1_center.xtc -os no_solv.xvg -select
'name OW and within 0.3 of group ser76' -n analyze.ndx*
This command gives an error
Error in user input:
Selection 'name OW and within 0.3 of group ser76' never matches any atoms.

2. Regarding *MMPBSA calculation* for my protein-ligand simulation. i m
using GROMACS 2018 version on the server. What is the procedure for doing
the same.

Thanks & Regards,
Dr. Pooja Kesari
Post Doctoral Fellow
Department Of Biosciences and Bioengineering
Indian Institute of Technology Bombay
INDIA