On Tue, Nov 21, 2017, sangita kachhap wrote:
>
> I have to do MD simulation of protein-metal ion complex employing bonded
> model MD simulation. I have generated topology file for the bonded model.
> When I am using CPU for calculations, its working fine but when using GPU
> its showing problem
> "3086: 6179 - 6180 and 3088: 6178 - 6180
> Hydrogen atom 6180 appears to have multiple bonds to atoms 6179 and 6180
> which is illegal for SHAKEH.
> Exiting due to the presence of inconsistent SHAKEH hydrogen clusters."
Use the printBonds command in parmed to see if these bonds indeed exist,
and if atom 6180 is indeed a hydrogen. Also run "checkValidity" inside parmed
to see if it spots any problems.
Also, search for this error at the Amber mailing list. These entries
might apply to you:
archive.ambermd.org/201609/0398.html
archive.ambermd.org/201609/0274.html
> In case if I will opt CPU for final calculation. Will it affect my expected
> result?
No.
...dac
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Received on Tue Nov 21 2017 - 05:30:02 PST
