Re: TypeError: string indices must be integers [NAMD psf,dcd gmx_MMPBSA]

[Mario Ernesto]

try with this command line:

gmx_MMPBSA -O -i mmpbsa.in -cs gromacs.pdb -ct traj.xtc -ci index.ndx -cg 3 2 -cp gromacs.top

you can use gmx make_ndx in gromacs to see the groups in the index file:

gmx make_ndx -n index.ndx

as you will see, the error occurs because groups 1 and 13 contain the same atoms... on the other hand, groups 3 and 2 contain the proteins and ligand atoms respectively...

let us know if that solves the problem...

cheers!

El lun, 28 mar 2022 a las 23:54, KyoungPyo Kwon (<kkp...@sunmoon.ac.kr>) escribió:

Greatings, all of my senior I'm undergraduate student in Korea

After protein with ligand molecular dynamics simulation using NAMD, i calculated gmx_MMPBSA based on the following psf_dcd tutorial such as 

https://valdes-tresanco-ms.github.io/gmx_MMPBSA/examples/psf_dcd/protein_ligand/

but i got a error like the figure.

So how can i resolve this error ?
I attach my file except xtc and dcd format file those have huge to load.

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[Mario Ernesto]

Great! :)

El mar, 29 mar 2022 a las 1:08, KyoungPyo Kwon (<kkp...@sunmoon.ac.kr>) escribió:

Thank u for kindly advice, immediately after a question i compare the my log file with tutorial results i found problem which based on group selection :) !
So i fixed -cg 3 2 it is working now ! Thanks a lot !

2022년 3월 29일 화요일 오후 3시 34분 12초 UTC+9에 marioe911116님이 작성: