msms assigns a van der Waals radius of 0

[hzy317]

Here is the translation of your request:

"Our code encountered some issues during execution. When processing pdb files, msms assigns a van der Waals radius of 0. How can we solve this problem?"

thanks for your help

root@2a420a30f6d9:/home/masif-neosurf-main/masif/data/masif_site# msms -if data_preparation/00-raw_pdbs/1MBN.pdb -of /tmp/1MBN_msms -probe_radius 1.5
MSMS 2.6.1 started on 2a420a30f6d9
Copyright M.F. Sanner (1994)
Compilation flags -O2 -DVERBOSE -DTIMING
Atom 1 ignored, radius = 0.000000
Atom 2 ignored, radius = 0.000000
Atom 3 ignored, radius = 0.000000
Atom 4 ignored, radius = 0.000000
GET_ATOMS: r missing on line 0 COMPND MOL_ID: 1;

Atom 6 ignored, radius = 0.000000
Atom 7 ignored, radius = 0.000000
Atom 8 ignored, radius = 0.000000
GET_ATOMS: r missing on line 0 SOURCE MOL_ID: 1;

Atom 10 ignored, radius = 0.000000
Atom 11 ignored, radius = 0.000000
GET_ATOMS: r missing on line 1 KEYWDS OXYGEN STORAGE

GET_ATOMS: r missing on line 1 EXPDTA X-RAY DIFFRACTION

GET_ATOMS: x[2] missing on line 1 AUTHOR H.C.WATSON,J.C.KENDREW

Atom 16 ignored, radius = 0.000000
Atom 17 ignored, radius = 0.000000
Atom 18 ignored, radius = 0.000000
Atom 19 ignored, radius = 0.000000
Atom 20 ignored, radius = 0.000000
Atom 21 ignored, radius = 0.000000
Atom 22 ignored, radius = 0.000000
Atom 23 ignored, radius = 0.000000
Atom 24 ignored, radius = 0.000000
Atom 25 ignored, radius = 0.000000
Atom 26 ignored, radius = 0.000000
Atom 27 ignored, radius = 0.000000
Atom 28 ignored, radius = 0.000000
Atom 29 ignored, radius = 0.000000
Atom 30 ignored, radius = 0.000000
Atom 31 ignored, radius = 0.000000
Atom 32 ignored, radius = 0.000000
Atom 33 ignored, radius = 0.000000
Atom 34 ignored, radius = 0.000000
Atom 35 ignored, radius = 0.000000
Atom 36 ignored, radius = 0.000000
Atom 37 ignored, radius = 0.000000
Atom 38 ignored, radius = 0.000000
GET_ATOMS: r missing on line 1 JRNL AUTH H.C.WATSON

Atom 40 ignored, radius = 0.000000
Atom 41 ignored, radius = 0.000000
Atom 42 ignored, radius = 0.000000
GET_ATOMS: x[2] missing on line 1 REMARK 1

Atom 45 ignored, radius = 0.000000
Atom 46 ignored, radius = 0.000000
Atom 48 ignored, radius = 0.000000
Atom 49 ignored, radius = 0.000000
Atom 51 ignored, radius = 0.000000
Atom 52 ignored, radius = 0.000000
Atom 54 ignored, radius = 0.000000
GET_ATOMS: r missing on line 5 REMARK 1 REFN

Atom 57 ignored, radius = 0.000000
Atom 58 ignored, radius = 0.000000
Atom 60 ignored, radius = 0.000000
GET_ATOMS: r missing on line 7 REMARK 1 REFN

GET_ATOMS: x[2] missing on line 7 REMARK 2

GET_ATOMS: x[2] missing on line 8 REMARK 3

GET_ATOMS: r missing on line 8 REMARK 3 REFINEMENT.

Atom 66 ignored, radius = 0.000000
Atom 67 ignored, radius = 0.000000
GET_ATOMS: x[2] missing on line 8 REMARK 3