Error in running "gmx_MMPBSA"

[Vishwambhar Bhandare]

Dear Sir ,

We are facing difficulties in running 'gmx_MMPBSA' for trajectory of modified tRNA with codon triplet. 

We get following error (refer attached screenshot)

 "MMPBSA_Error: The receptor index has fewer atoms than the topology. Please check that the files are consistent." 

We have also crosschecked all the input files manually for the atom number mismatch. 

I request you to please check our files and suggest possible solutions. 

Here, our com.top is a topology of complex without solvent. The file "AAA.top" is topology of ligand, "ASL.top" is the topology of receptor and "com_solv_N.top" is the topology of solvated complex.

Looking for your support in this regard. 

Thanking you, 

Sincerely, 

Vishwambhar

[marioe911116]

could you please send the structure file (tpr or pdb) you are using?

[Vishwambhar Bhandare]

Please find attached tpr file. 

[Vishwambhar Bhandare]

[marioe911116]

Using this command line, it works fine:

gmx_MMPBSA -i mmpbsa.in -cs md.tpr -ct bf1.xtc -ci index.ndx -cg 0 1 -cp com.top

Of note, the trajectory has PBC and in theory, this should be corrected before running the calculations...

let me know if this solves the issue...

cheers!