Re: [AMBER] atom number difference in topology and simulated trajectory

From: Elvis A F Martis <>
Date: Sat, 27 Feb 2021 15:16:44 +0530

if you are directly passing the solvated trajectory to, don't
forget to use -sp <solvated_trajectory>.prmtop

On Saturday, 27 February 2021, Ayesha Fatima <>

> Dear all,
> I have a query regarding the above subject.
> I prepared my solvated and unsolvated complex and other required files for
> simulation. the simulation ran fine. Now when i want to calculate the
> mmpbsa, the error comes for the difference in number of atoms between
> topology and trajectory files. my simulation generated the .nc trajectory
> and used the script for calculation. I have started the
> simulation again but it will take some time now.
> Is there a workaround?
> Thank you
> Regards
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Received on Sat Feb 27 2021 - 02:00:02 PST
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