Re: error while running gmx-MMPBSA

[marioe911116]

it should be with "-i mmpbsa.in"

gmx_MMPBSA -O -i mmpbsa.in -cs md_0_100.tpr -ci index.ndx -cg 1 13 -ct md_0_100_center.xtc -cp topol.top

El viernes, 10 de marzo de 2023 a las 3:29:02 UTC-7, deepas...@gmail.com escribió:

Sir,

While running the command "gmx_MMPBSA -O i mmpbsa.in -cs md_0_100.tpr -ci index.ndx -cg 1 13 -ct md_0_100_center.xtc -cp topol.top" I am facing an error. Kindly help me solve the issue.

[Mario Ernesto]

There was a typo in the command line... The flag for the input file mmpbsa.in is "-i"

On Fri, Mar 10, 2023, 9:48 a.m. DEEPASREE K <deepas...@gmail.com> wrote:

I couldn't get you. Can you explain it more clearly?

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[marioe911116]

the *.xtc with the PBC conditions removed, whichever that is (I assume is md_0_1_center.xtc)

El viernes, 10 de marzo de 2023 a las 10:29:41 UTC-7, deepas...@gmail.com escribió:

Which xtc file should we choose while running gmx_MMPBSA command : md_0_1.xtc or md_0_1_center.xtc?

[DEEPASREE K]

Thank you.

[Mario Sergio Valdes]

Which ff did you use to parameterize your system? Note that only AMBER and CHARMM and fully supported, while OPLSAA is supported with limitations. Other ff like GROMOS are not supported

El viernes, 10 de marzo de 2023 a las 23:08:42 UTC-5, deepas...@gmail.com escribió:

i am getting another error while running the command " gmx_MMPBSA -O -i mmpbsa.in -cs md_0_100.tpr -ci index.ndx -cg 1 13 -ct md_0_100_center.xtc -cp topol.top".

[Mario Sergio Valdes]

Unfortunately, at the moment, GROMOS ff is not supported. You can use another tool like g_mmpbsa or GMXPBSA2.1or you can use another method to compute the BFE. We will implement it soon, but it will take a while yet.

El viernes, 10 de marzo de 2023 a las 23:28:53 UTC-5, deepas...@gmail.com escribió:

I used gromos96 43a1 forcefield. What should I do now?

[DEEPASREE K]

Okay. Thank you.