(Alanine Scanning) issues with creating alanine input file & tleap failed when querying _GMXMMPBSA_leap.in

[Muhamad Alif Bin Che Nordin]

Hey guys!

I tried to perform alanine scanning onto my protein-protein (chain A+B against C). FYI, I did the simulation on coarse-grain then i reverse transform back into all-atomic structures before performing any analysis. I calculated &decomp and found my residue of interest on Chain A. 

First issue:

I tried to use --create_input to create alanine scanning input file but it came out like this:

I wonder what went wrong?

Second issue: So i proceed with sample input file and define my mutant_res.

When i proceed with alanine scanning, i received this error.

Attached here are the log files.

Can you please tell me how can i proceed from here?

thanks

[marioe911116]

If you want to create an input for alascan you need to define which model to use (gb or pb)... for instance for gb and alascan will be as follows:

gmx_MMPBSA --create_input gb ala

and for the second error, please, use the -cp topol.top flag

[Muhamad Alif Bin Che Nordin]

got it. thanks a lot

alif

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ALIF NORDIN.

Assistant Registrar N41
PJK, UniSHAMS

04-4155095

0174070407

01140737157

Bachelor of Biomedicine (Hons.), Master of Science (Biomedicine)

Cancer Immunology · Medical Virology · Molecular Dynamics Simulation

Ordinary Member of Malaysian Society for Biochemistry and Molecular Biology (MSBSB) [Membership No. OM-2019-044]

Pusat Jaminan Kualiti
Universiti Islam Antarabangsa Sultan Abdul Halim Mu'adzam Shah  (UniSHAMS)