Hello,
since the top files do not look valid, just a guess/hint:
- Did you check your inputs for any peculiarities and formatting problems?
- Are the parameter files you generated ok?
- Did antechamber recognize the elements correctly and assign rational
atom types?
- Did leap print any warnings?
I'd suggest to take a single problematic ligand, run all step by step,
and inspect the intermediate output files and messages.
But maybe others have encountered this type of problem before.
Best,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
On 02/27/2024 05:09 PM, Trevor Kramer via AMBER wrote:
> Hello,
>
> We have been running a large number of ligands through amber recently and have encountered a few instances that have generated prmtop with large values in the ATOMIC_NUMBER block in the prmtop file as shown below. These cause errors with mdanalysis and loading into VMD.
>
> [F2kRSxtgHYx9EDox9qEL78D9AZ4dtdG4ghQAAAABJRU5ErkJggg==]
>
>
>
> We are using the latest release of ambertools.
>
> Thanks,
> Trevor and Levi
>
>
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Received on Wed Feb 28 2024 - 03:30:02 PST
