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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
