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[Question]: bad atom type: Pb and sander failed with prmtop COM.prmtop! #556

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TuLingZb opened this issue Jan 3, 2025 · 4 comments
Open

[Question]: bad atom type: Pb and sander failed with prmtop COM.prmtop! #556

TuLingZb opened this issue Jan 3, 2025 · 4 comments

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@TuLingZb
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TuLingZb commented Jan 3, 2025

My Question is...

Hello I have run a simulation for a nucleic-mental complex using amber99SB force field in GROMACS and when I tried to run gmx_MMPBSA it gave me this error, can someone help me T_T
@Valdes-Tresanco-MS
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Which error? Please, attach the gmx_MMPBSA.log file

@marioernestovaldes
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Please, check this thread https://groups.google.com/g/gmx_mmpbsa/c/YeTDAbXvurQ/m/BToWonT3AQAJ

@TuLingZb
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TuLingZb commented Jan 7, 2025

My log file is here.

gmx_MMPBSA.log

Which error? Please, attach the gmx_MMPBSA.log file

@TuLingZb
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TuLingZb commented Jan 7, 2025

The methods mentioned in the link are difficult for me to execute. any alternative feasible methods?

Please, check this thread https://groups.google.com/g/gmx_mmpbsa/c/YeTDAbXvurQ/m/BToWonT3AQAJ

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@Valdes-Tresanco-MS @marioernestovaldes @TuLingZb