Alanine Scanning: Multiple Residues & Using previous data

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Uddipta Ghosh Dastidar

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Jul 24, 2025, 3:04:27 AMJul 24
to gmx_MMPBSA
While using the Alaning Scanning of the programme, it usually generates three sets of data.  
(1) Normal , (2) Mutated, and (3) Mutated - Normal

My questions are,

a. I have already run a MMGBSA, (which is basically the normal or un-mutated one), and later decided to run only the Alanine Scanning of a residue separately.
How can I indicate the programme to  consider the previous MMGBSA data for the Normal Non-mutated part, without repeating it again for scanning calculation. (Obviously I will keep other parameters, time, interval, temp, ff, etc same). It will save a lot of time.

b. Can alanine scanning of two residues be done in one go? Like by adding consecutive lines in the same input file?
..

&alanine_scanning
mutant= 'ALA', mutant_res= 'A/123' , cas_int_diel=1
/
&alanine_scanning
mutant= 'ALA', mutant_res= 'A/321' , cas_int_diel=1
/

Thanking you in anticipation.

marioe911116

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Jul 24, 2025, 3:23:41 AMJul 24
to gmx_MMPBSA
a- Calculations can be performed for the mutant only using mutant_only=1 in the input file under the alascan namelist but you will have to process the difference later on your own:
b- Unfortunately, no.
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