Processing chain 1 ‘A’ (1364 atoms, 163 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 273 donors and 248 acceptors were found.
There are 347 hydrogen bonds
Will use HISD for residue 31
Identified residue MET1 as a starting terminus.
Identified residue ASN163 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
MET1 MET6 HIS31 CYS54 CYS97 MET106
SD10 SD56 NE2276 SG446 SG808 SD883
MET6 SD56 0.631
HIS31 NE2276 2.196 1.931
CYS54 SG446 2.781 2.718 1.052
CYS97 SG808 0.820 0.539 2.117 2.897
MET106 SD883 1.900 1.314 1.848 2.841 1.635
MET120 SD982 2.525 2.014 3.286 4.293 2.112 1.520
Start terminus MET-1: MET1
End terminus ASN-163: COO-
Program: gmx pdb2gmx, version 2021.4-Ubuntu-2021.4-2
Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1104)
Fatal error:
atom C1 not found in buiding block 1MET while combining tdb and rtp
For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation