Open Jiang-Lu-CAS opened 6 months ago
I encountered the same problem.
It seems that the implementation of the path to the index file provided for the water system in prepare_dual_topology.py
is incorrect.
For example, in runall_FXR_12-FXR_74_water.sh
, tutorial/FXR_12-FXR_74/protein/build_system_*/index.ndx
is specified, but this should actually specify tutorial/FXR_12-FXR_74/water/build_water_*/index.ndx
.
I encountered the same problem. It seems that the implementation of the path to the index file provided for the water system in
prepare_dual_topology.py
is incorrect. For example, inrunall_FXR_12-FXR_74_water.sh
,tutorial/FXR_12-FXR_74/protein/build_system_*/index.ndx
is specified, but this should actually specifytutorial/FXR_12-FXR_74/water/build_water_*/index.ndx
.
@YumizSui Yes, I corrected it by hand and it worked after I replace the protein index to the right water index. Unfortunately, it failed again in the analysis step, which looked like the water file missed several code compared with the protein run file. The author should correct the code. Have you run it completely? How did you solve the problems? Thanks.
Hi, I failed in the "bash runall.sh" step. The protein file worked well but the water file failed in the nvt process. Here are the details in nvt_grompp.log.
After check, I found it's due to the wrong index file (protein/..)
Can you help us solve this problem. Thanks.
Jiang