Chain assignment while running Alanine scanning

[gagandeep singh]

Dear Mario,

I hope you are doing fine. I am trying to run the alanine scanning for my protein-ligand system but it is giving a chain defining error. My protein is a single chain structure and chain ID is not assigned  to it. I used a reference structure with flag -cr md.pdb but it is still asking for chain assignment in the format chain: residue number. Then I used assign_chainID = 1 flag in &general but it is also giving the same error. Can you pls suggest how I should proceed in this case?




Thanks and regards

Gagandeep Singh


--

Assistant Research Officer (Biotechnology)

Central Ayurveda Research Institute, Jhansi

Ph.D. Scholar

KSBS, IIT Delhi

Mob- 8178163366, 8285477478

[Mario Ernesto]

Hi there! could you please send around the files you are using, so we can check if there is something going wrong with the code?

cheers!

Mario E.

--
You received this message because you are subscribed to the Google Groups "gmx_MMPBSA" group.
To unsubscribe from this group and stop receiving emails from it, send an email to gmx_mmpbsa+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/gmx_mmpbsa/CACL%3Dysb3d-SenBMue25UjG1z2a2LCnD451NyE10TvFszwZtkpw%40mail.gmail.com.
For more options, visit https://groups.google.com/d/optout.

[marioe911116]

I received your files. The thing is the variable 'assign_chainID' is ignored when you pass a reference structure... in this case, your reference structure doesn't contain the chain IDs either and that's why gmx_MMPBSA end up in error... just add the chain IDs to your reference structure 'md.pdb' (A for the protein and B for the ligand for instance) and also make sure your mmpba.in file has the proper notation for the mutant (see bold letters). I also see you are specifying 'startframe=9900, endframe=10000', remember this refers to frames and not time, so if your trajectory has 10000 frames that's ok... if not make sure 'startframe' and 'endframe' are defined according to the number of frames you are analyzing in the trajectory...

Sample input file for entropy calculations

#This input file is meant to show only that gmx_MMPBSA works. Althought, we tried to used the input files as recommended in the 

#Amber manual, some parameters have been changed to perform more expensive calculations. Feel free to change the parameters 

#according to what is better for your system.

&general

#

startframe=9900, endframe=10000, interval=1,assign_chainID = 1

protein_forcefield="oldff/leaprc.ff99SB",

/

&gb

igb=2, saltcon=0.150,intdiel=8

/

&alanine_scanning

mutant='ALA'

mutant_res='A:240'

/

hope this helps!

cheers!