[Bug-gmx_MMPBSA]: The complex index has fewer atoms than the topology. Please check that the files are consistent.

[ChenHiuhong1]

Bug summary

I get this error after I enter the following command in the Linux terminal: The complex index has fewer atoms than the topology. But after I checked m data.zip y topology file, the atomic numbers are consistent.

Terminal output

gmx_MMPBSA -O -i mmpbsa_mem.in -cs sys.pdb -ci 2.ndx -cg 1 13 -ct mdnopbc.xtc -cp topol.top

gmx_MMPBSA.log

gmx_MMPBSA.log

Operating system

CentOS 7

gmx_MMPBSA Version

v1.5.0.3

Python version

3.12.2

Installation

conda AmberTools + conda

[ChenHiuhong1]

The xtc file is too big, I can send it to you by mail if you need it

[ChenHiuhong1]

Then I tried several times and I still couldn't fix the error. I have no idea about this.

[marioernestovaldes]

I see you have lipids in your system, please remove those form teh topology and the input files before performing the calculations. at the end they are not used as you are using implicit membrane conditions. Once you delete the lipids form the input files (strcuture, tracjetory, and topology) create a fresh new index fioe and try again

[ChenHiuhong1]

So can I keep TIP3P and POT and CLA components？

[marioernestovaldes]

You don't have to, they are no needed for the calculations

[ChenHiuhong1]

There is a new error gmx_MMPBSA.log

[ChenHiuhong1]

In this calculation, my topology file and trajectory, the structure retains only the protein component and the UNL component

[marioernestovaldes]

Please update gmx_MMPBSA to teh last version:

python -m pip install gmx_MMPBSA -U

if you get nay error, please post the error here

[ChenHiuhong1]

Thanks, I am updating the gmx_MMPBSA now.Then I will try again

[ChenHiuhong1]

note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pandas Successfully built matplotlib Failed to build pandas ERROR: Could not build wheels for pandas, which is required to install pyproject.toml-based projects

[ChenHiuhong1]

and in the terminal: IndexError: list index out of range

[marioernestovaldes]

Please post a picture of the error

[ChenHiuhong1]

[ChenHiuhong1]

The first picture：when i use tpr file,it occurs this error.after i change the reference strcuture to the first frame in trajectory, the mmpbsa can run.But I'm not sure if I'll report an error in the future. because i still use the 1.5.0.3 mmpbsa The second picture: when i used "python -m pip install gmx_MMPBSA -U "to update mmpbsa, it occurs this error

[marioernestovaldes]

Hmmm... its best if you send me the files and I see exactly what's going wrong. As per the new gmxMMPBSA installation, did you create a new fresh conda envorinment and follow all the instruction here:

https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/installation/

[ChenHiuhong1]

First I use the gro file generated by molecular dynamics simulation to generate the protein_unl index group：2_produce_from_gro.ndx Next, I use this index file to generate a tpr file with only the protein_unl index group - gmx convert-tpr -s md_100ns.tpr -n 2_produce_from_gro,ndx -o md.tpr Then,I used a new tpr file to generate the "nopbc" xtc file containing only protein_unl, that is mdnopbc.xtc Then I used a trajectory that is generated by this output to gain the reference struture:gmx trjconv -s md_100ns.tpr -f md_100ns.xtc -pbc cluster - center , choose protein_unl protein_unl system.I extract the structure at 60000ps in this trajectory：lastmem60ns.pdb. At last, I used md.tpr to generate the new index file that contains protein_unl, the index file is 3.ndx mmpbsa.zip

[ChenHiuhong1]

About installation, I did not create a new environment, I will try again. Thanks!