Error in topology file -Charmmff

[Anis Nadyra Ahmad Zifruddin]

Hi,

I encounter a problem as below;

MMPBSA_Error: The atom 4056 in the complex index is not found in the topology file. Please check that the files are consistent.

For your information, some of the complex works, but the other persistently encounter this problem. I attach .log file, topol.top and .itp file for your reference.  Thank you for your help!

[marioe911116]

could you please share the "step5_1.tpr" file?

[Mario Sergio Valdes]

According to the index file, the receptor (GMXMMPBSA_REC) has 4002 atoms, while the ligand (GMXMMPBSA_LIG) has 53 for a total of 4055 atoms (GMXMMPBSA_REC_GMXMMPBSA_LIG). In this case, it is probably an error in the index or the topology processing. To check this, our recommendation is to generate a new index from the tpr you used for the MD. In any case, you can send us the files to check if it is a problem with the index or of gmx_MMPBSA.

[Anis Nadyra Ahmad Zifruddin]

Hi Mario,
This is my step5.1.tpr file and index.ndx.

[Anis Nadyra Ahmad Zifruddin]

Sorry Mario,

This is the right index file.

Anis

On Tuesday, 17 May 2022 at 12:51:57 UTC+8 mariosergi...@gmail.com wrote:

[Mario Ernesto]

could you please also send the toppar folder associated with the topology file?

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[Anis Nadyra Ahmad Zifruddin]

Here is my toppar folder.

[Mario Ernesto]

We found the issue!  we'll get back to you asap with a solution... :)

[Mario Ernesto]

Could you please send 5 frames of your trajectory file ? We are working on a work around for your issue 

Thanks 

[Anis Nadyra Ahmad Zifruddin]

Here are my trajectory files for 5 frames.

[Mario Ernesto]

sorry for the misunderstanding... I need an xtc file with 5 frames...

thanks in advance

El mar, 17 may 2022 a las 22:00, Anis Nadyra Ahmad Zifruddin (<anisna...@gmail.com>) escribió:

Here are my trajectory files for 5 frames.

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[Anis Nadyra Ahmad Zifruddin]

This is xtc file with5 frames. Tq

[marioe911116]

your *.tpr file has a peculiar structure with CL ions between the protein and the ligand... gmx_MMPBSA is not prepared to deal with this kind of structure (we plan to improve this in future versions)... in the meantime, you can use this workaround to perform the calculations...

you need the tpr file (step5_1.tpr), the trajectory file (1.xtc in this case),  the mmpbsa.in file and the topol.top file with the associated toppar folder:

1-generate a index file with the complex group:

gmx make_ndx -f step5_1.tpr -o index.ndx

>1|14

>q

2-save the complex structure (as str.pdb) using 1.xtc trajectory:

echo 16 | gmx trjconv -f 1.xtc -s step5_1.tpr -n index.ndx -o str.pdb -dump 0

3-generate trajectory only with protein-ligand complex:

echo 16 | gmx trjconv -f 1.xtc -s step5_1.tpr -n index.ndx -o traj.xtc

4-generate index file with the new str.pdb file:

gmx make_ndx -f str.pdb -o index_1.ndx

>q

5-perform the calculation (with the new str.pdb, index_1.ndx and traj.xtc files):

gmx_MMPBSA -O -i mmpbsa.in -cs str.pdb -ci index_1.ndx -cg 1 13 -ct traj.xtc -cp topol.top -eo output -nogui

hope this helps!