Kindly explain me this error and provide an elaborate explanation and
fix.
Thank you so much. Your help is much needed.
Regards,
Priyasha Majee
On 2025-11-20 19:35, Tomás Benjamín Cáceres Madariaga wrote:
> Hi, this link contains relevant information about your issue.
> http://archive.ambermd.org/202411/0053.html
>
> Tomás Cáceres
> Bioquímico UC
> Asistente de Investigación | Laboratorio de Simulación Computacional y
> Diseño de Fármacos
>
> -------------------------
>
> From: Priyasha Majee via AMBER <amber.ambermd.org>
> Sent: Thursday, November 20, 2025 9:45 AM
> To: Amber <amber.ambermd.org>; Majee Priyasha123
> <majee.priyasha123.gmail.com>
> Subject: [AMBER] Bad atom type
>
> Dear All,
>
> I am trying to do MMGBSA/MMPBSA per-residue decomposition in AMBER. My
> system is G-Quadruplex-small ligand complex. The G-Quadruplex has K+
> ions in the core. The system was solvated and K+ ions were added to
> neutralize the system. When I am trying to run the MMPBSA calculation,
> it is throwing an error:
>
> Bad atom type: K+
>
> After searching extensively, I opted for a fix. I attempted to manually
> correct the atom type from K+ to K in a text editor for the (-sp)
> solvated complex and (-cp) no-water-complex.prmtop files. I would like
> to mention that the indentations were all taken care of. After running
> the calculation, it stopped throwing the same error but for K now:
>
> Bad atom type: K
>
> My logic was to rename the K+ to K to maintain the number of atoms in
> solvated_complex.prmtop with the solvated trajectory. Removing the ions
> will decrease the atom count when compared to trajectory.nc. I tried
> this and it showed an error.
>
> kindly help me with bad atom type error. why is it happening and what
> could be the potential fix?
>
> Thanks
>
> Regards,
>
> Priyasha Majee
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Received on Thu Nov 20 2025 - 21:30:03 PST
