I ran Generalized Born (GB) with quasi-harmonic calculations for a 20 amino acid (AA) peptide and a 400 AA long antibody complex using 101 frames.
However, my terminal has been in this state for about 2 hours with my CPU running continuously.
Is this normal, or could there be some kind of error occurring? I have copied my command lines below with pictures. Any help would be greatly appreciated.
[INFO ] Selecting residues by distance (10 Å) between receptor and ligand for decomposition analysis...
[INFO ] Selected 102 residues:
R:A:GLY:1 R:A:GLU:2 R:A:GLU:3 R:A:SER:4 R:A:ALA:5 R:A:SER:6 R:A:SER:7 R:A:GLY:8 R:A:LYS:9 R:A:LEU:10
R:A:GLY:11 R:A:LEU:12 R:A:ILE:13 R:A:THR:14 R:A:ASN:15 R:A:THR:16 R:A:ILE:17 R:A:ALA:18 R:A:GLY:19 R:A:VAL:20
R:A:ALA:21 R:A:GLY:22 R:A:LEU:23 R:A:ILE:24 R:A:THR:25 L:B:GLN:1 L:B:LEU:2 L:B:VAL:3 L:B:LEU:24 L:B:SER:25
L:B:ARG:26 L:B:GLN:27 L:B:HIS:28 L:B:SER:29 L:B:THR:30 L:B:TYR:31 L:B:THR:32 L:B:ILE:33 L:B:GLU:34 L:B:TYR:36
L:B:TYR:46 L:B:MET:48 L:B:GLU:49 L:B:LEU:50 L:B:LYS:51 L:B:LYS:52 L:B:ASP:53 L:B:GLY:54 L:B:SER:55 L:B:HIS:56
L:B:SER:57 L:B:SER:70 L:B:GLY:72 L:B:ARG:75 L:B:GLY:93 L:B:VAL:94 L:B:GLY:95 L:B:ASP:96 L:B:THR:97 L:B:ILE:98
L:B:LYS:99 L:B:GLU:100 L:B:GLN:101 L:B:PHE:102 L:B:VAL:103 L:B:TYR:104 L:B:ALA:159 L:B:PHE:160 L:B:SER:161 L:B:SER:162
L:B:TYR:163 L:B:ASP:164 L:B:MET:165 L:B:SER:166 L:B:TRP:178 L:B:ALA:180 L:B:TYR:181 L:B:ILE:182 L:B:SER:183 L:B:ARG:184
L:B:GLY:185 L:B:GLY:186 L:B:GLY:187 L:B:TYR:188 L:B:THR:189 L:B:TYR:190 L:B:ARG:203 L:B:ASN:205 L:B:SER:228 L:B:ARG:229
L:B:HIS:230 L:B:ILE:231 L:B:TYR:232 L:B:TYR:233 L:B:GLY:234 L:B:SER:235 L:B:SER:236 L:B:HIS:237 L:B:TYR:238 L:B:TYR:239
L:B:ALA:240 L:B:MET:241
[INFO ] Cleaning normal complex trajectories...
[INFO ] Building AMBER topologies from GROMACS files... Done.
[INFO ] Loading and checking parameter files for compatibility...
[INFO ] Preparing trajectories for simulation...
[INFO ] 101 frames were processed by cpptraj for use in calculation.
[INFO ] Starting calculations in 9 CPUs...
[INFO ] Running calculations on normal system...
[INFO ] Beginning GB calculations with /Users/mkkim/mambaforge/envs/gmx_MMPBSA/bin/sander
[INFO ] calculating complex contribution...
100%|##########| 101/101 [elapsed: 01:20 remaining: 00:00]
[INFO ] calculating receptor contribution...
100%|##########| 101/101 [elapsed: 00:03 remaining: 00:00]
[INFO ] calculating ligand contribution...
100%|##########| 101/101 [elapsed: 01:36 remaining: 00:00]
[INFO ] Beginning quasi-harmonic calculations with /Users/mkkim/mambaforge/envs/gmx_MMPBSA/bin/cpptraj
