# atoms in XTC file (3112) does not match # atoms in parm COM.prmtop (3122)

li tao

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Nov 10, 2021, 9:55:05 AM11/10/21

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we have two ligands (FMN and allurared), and a protein. I encounted the errors when using gmx_MMPBSA, Those errors are listed as below:

Error: # atoms in XTC file (3112) does not match # atoms in parm COM.prmtop (3122)

And my command is: gmx_MMPBSA -O -i mmpbsa.in -cs md01.pdb -ci index.ndx -cg 1 13 -cg 1 14 -ct md01.xtc -lm FMN_gaff.mol2 -lm allurared_gaff.mol2.

li tao

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Nov 10, 2021, 10:02:04 AM11/10/21

to gmx_MMPBSA

index.ndx

gmx_MMPBSA.log

mmpbsa.in

md01.tpr

Mario Sergio Valdes

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Nov 10, 2021, 10:55:06 AM11/10/21

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I don't fully understand what you want to do.

The command-line options are unique, so repeating it will not have the effect you want, but only the values of the last definition will be taken.

Currently, gmx_MMPBSA does not support the generation of Amber topologies based on the definition of multiple ligands (mol2). This represents the error you report. In this case, you must use topology conversion (-cp option).

To calculate the free energy value for each ligand, you must do it independently, that is, one calculation for each ligand. You can do a per-residue to estimate the contribution of each ligand to the binding free energy of the other.

Be careful with the values of the variables defined in the mmpbsa.in file. The variable intdiel is usually between 1 (for hydrophobic molecules) and 10 (for highly charged molecules), with values of 1 and 4 being more frequent. The one you are using is extremely large.

Sincerely

Mario S.

El miércoles, 10 de noviembre de 2021 a las 10:02:04 UTC-5, taol...@gmail.com escribió:

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