Lei Qian

@Valdes-Tresanco-MS Thanks! It works. Actually when I ran regular GB only, I did not include my own topology files in working directory (and did not use -cp flag), and they...

@Valdes-Tresanco-MS @marioernestovaldes Thanks very much for your kind replies. I really appreciate it. I reran the system using , and found the results were similar as , so I think...

@Valdes-Tresanco-MS Thank you for your reminding. I read the paper (Yan 2017). From my understanding, when I run regular GB, default intdiel (Internal dielectric constant) is 1.0, which can be...

@Valdes-Tresanco-MS @marioernestovaldes Thank you for your explanation! As @Valdes-Tresanco-MS mentioned "so using them (system-dependent parameters) requires a thorough study of the system characteristics". Because intdiel is one of system-dependent parameters,...

@Valdes-Tresanco-MS @marioernestovaldes Thanks! I will reread this Yan et al. paper and try to find the suitable intdiel value for my system and figure it out.

@Valdes-Tresanco-MS @marioernestovaldes Hope everything is going well. These days I compared ddG results calculated by both alanine scan and regular GBSA (WT => Ala mutant) (intdiel were set to the...

Hi @Valdes-Tresanco-MS Thank you for your suggestion I tried $ which bash, and it is "/usr/bin/bash" and I tried to change double brackets pair [[ ]] to single bracket pair...

@Valdes-Tresanco-MS Thanks! Problem solved