If you are using sander and PB calculation, check the *.mdout files to get the sander error

[Subha Yegnaswamy]

Hi All,

I am getting a sander and PB calculation error.

I am working on a membrane protein.Prepared the membrane using charmm-gui builder.After that i did simulation using Gromacs2021.1 version.I am trying to calculate the membrane and protein interaction using MMPBSA.

I am calculating only one frame  as i understood from the groups it is RAM expensive calculation.

Please find attached gmxmmpbsa.in file and *.mdout file and some output files for reference.

when i uncomment PDBradii for charmmff i am getting a radii error. so i commented it again.  I have kept the protein in the middle of the membrane.

Why i am getting this error?

I have already checked the discussion groups regarding this. I am trying for more than a week..Please help. Pls let me know if you need more information.

Thank you for your support.

Best Regards,

Subha.

[Mario Ernesto]

Please, check this thread:

https://groups.google.com/g/gmx_mmpbsa/c/UqImUx8hCI0/m/orUsFBNCAAAJ

try changing cutnb parameter to a lower value (e.g. 9) and increase linit to 10000

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[Subha Yegnaswamy]

Hi,

Thank you for yesterday's reply to sander and PB calculation error.

I modified the mmpbsa.in file for my membrane protein input.I am using a complex lipid bilayer.CHL,POPC,POPI,POPS,POPE etc., 

Because of intensive calculation required for complex bilayer, i  have selected only one of the membrane component cholesterol for calculation.Planning to do all the other lipid bilayer separately.

After selecting only cholesterol as ligand, it is calculating but the o/p files are not generated. It is giving a mathdomain error.

Please find attached the output file with the error and the log file.

How should i solve this one.

Thank you for your support.

Subha.

[Mario Ernesto]

Are you selecting all cholesterol molecules as ligand? if so, gmx_MMPBSA and the methodology are not designed to consider that, instead, you could select only a molecule of cholesterol of interest

To view this discussion on the web visit https://groups.google.com/d/msgid/gmx_mmpbsa/d130c9fe-311b-4d62-b6d6-9efb80ccf0d8n%40googlegroups.com.

[marioe911116]

Closing this thread as it was solved offline

you can use inp=1 to get negative energies

https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/Q%26A/calculations/#possible-solutions_2

El lun, 6 nov 2023 a las 1:19, Subha Yegnaswamy (<subha.ye...@dypatil.edu>) escribió:

Hi,

Thank you Mario. I got the results with 4 frames.

PFA the output file.

I will try now with the other lipids POPC molecule.

I was just breaking my head for this:)

Pls have a look if the results are looking good.

Many thanks for your help.

Best Regards,

Subha.

On Mon, Nov 6, 2023 at 12:40 PM Mario Ernesto <marioe...@gmail.com> wrote:

Have you tried with more than 2 frames, let's say 5? also, this kind of error is usually indicative that something is off with the calculation

El lun, 6 nov 2023 a las 0:07, Subha Yegnaswamy (<subha.ye...@dypatil.edu>) escribió:

Hi Mario,

Thank you for your mail.

I did not attach the output file in my last mail.

To remind you, i m working on membrane-protein interaction.

The gmx-MMPBSA is calculating the file, but iam getting an error while generating the output.

Please find attached my output file.

Thanks in advance for your time and support.

Best Regards,

Subha.

To view this discussion on the web visit https://groups.google.com/d/msgid/gmx_mmpbsa/CAEewqyrZVMn7zkckiHEec3O0_n70RzQxaR6WHzgrQBixanaz2w%40mail.gmail.com.

For more options, visit https://groups.google.com/d/optout.

--

Subha Yegnaswamy,

Ph.D student,

Department of Bioinformatics, 

School of Biotechnology and Bioinformatics,

D Y Patil Deemed to be University,

Plot 50, Sector 15, CBD Belapur, 

Navi Mumbai 400614, INDIA

--

Subha Yegnaswamy,

Ph.D student,

Department of Bioinformatics, 

School of Biotechnology and Bioinformatics,

D Y Patil Deemed to be University,

Plot 50, Sector 15, CBD Belapur, 

Navi Mumbai 400614, INDIA