Dear all,
I used CGenFF to generate .str file, but it gave me the one with high penalties.
Could you please tell me how I can validate that file to reduce penalties?
As there was no response in this regard I look forward to hearing from you.
I apperciate your responses in advance.
Best
The CGenFF papers (the original in JCC in 2010 and subsequent papers in JCIM in 2012) walk through how to parametrize molecules and what the penalties mean. The FFParam GUI may be useful here, at least in terms of generating QM and MM inputs for the required calculations (none of which are done in GROMACS).