Can I include pdb chains A and C to index.ndx using Gromacs gmx make_ndx?

User discussions
1

GROMACS version: 2019.2
GROMACS modification: No

hello everybody,

I am trying to create a Gromacs index using

gmx make_ndx -f …/inici/AAAKTPVIV_HLA_A_02_01.pdb -o index.ndx

and I want to include chains A and C to the index

I just tried to do it using the following commands

chain A

chain ‘A’

‘chain A’

etc

but it fails all the time

Found 0 atoms with chain identifier A (idem for C)

Group is empty

Of course, I checked that my PDB has chains A and C (it also has B)

Can any want tell me how to deal with it?

Thanks in advance!

2

HI,
In 2019 version there was a bug connected to gmx make_ndx and chain recognition (see release note for 2019.4 http://manual.gromacs.org/current/release-notes/2019/2019.4.html)

Please update to the current version

or if your work requires 2019 use 2019.6

Best regards
Alessandra

3

thank you for your recomendation