Local structure index of water (LSI) code issue

[Saqlain5565]

i have been trying to get Local structure index (LSI) of water TIP4P/EW by running NPT through cpptraj by using following commands.

parm tip4p/ew.parm7
trajin eq_npt.nc
solvent :WAT
hbond watcoord out water_coordination.dat
run

but following warning comes without output file.

Warning: Nothing selected for hydrogen bond analysis.
Warning: Setup incomplete for [hbond]: Skipping

Warning: Set 'WATcoord[UU]' contains no data.
Warning: File 'water_coordination.dat' has no sets containing data.

can anyone tell me where the problem is?

or can provide correct code to get LSI of water .

[drroe]

By default, cpptraj will only look for solute-solute hydrogen bonds. If you want to explicitly look at water-water hydrogen bonds, you need to explicitly specify the water donors and acceptors:

hbond watcoord donormask :WAT@O acceptormask :WAT@O image out nhbvtime.dat avgout hbavg.dat

You probably want the image keyword so you can capture hydrogen bonds that cross unit cell boundaries. Note that this will produce tons of information in the avgout file, since every existing water-water hydrogen bond will be reported. It will also be fairly slow, so you may want to use the OpenMP or MPI/OpenMP hybrid code to speed things up.

Let me know if this helps.

[Saqlain5565]

Hello, Thanks for the response. what if i want to give specific boundary condition on 3.7Å ? then how can i change in that code ?

…

________________________________ 보낸 사람: Daniel R. Roe ***@***.***> 보낸 날짜: 2023년 8월 3일 목요일 오후 9:39 받는 사람: Amber-MD/cpptraj ***@***.***> 참조: Zafar,Muhammad Saqlain ***@***.***>; Author ***@***.***> 제목: Re: [Amber-MD/cpptraj] Local structure index of water (LSI) code issue (Issue #1043) By default, cpptraj will only look for solute-solute hydrogen bonds. If you want to explicitly look at water-water hydrogen bonds, you need to explicitly specify the water donors and acceptors: hbond watcoord donormask ***@***.*** acceptormask ***@***.*** image out nhbvtime.dat avgout hbavg.dat You probably want the image keyword so you can capture hydrogen bonds that cross unit cell boundaries. Note that this will produce tons of information in the avgout file, since every existing water-water hydrogen bond will be reported. It will also be fairly slow, so you may want to use the OpenMP or MPI/OpenMP hybrid code to speed things up. Let me know if this helps. — Reply to this email directly, view it on GitHub<#1043 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A7RA7U7UNJNY4DK43BEK2ITXTOLZXANCNFSM6AAAAAA3CJ2ELE>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[Saqlain5565]

The code provide the out.dat files which contains the avg angle 165 apx. but the Angle Cutoff = 135.000.

so is it acceptable to have angle apx 165?