Re: [AMBER] SHAKEH problem in GPU calculation

From: David A Case <>
Date: Tue, 21 Nov 2017 08:17:11 -0500

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:

> In case if I will opt CPU for final calculation. Will it affect my expected
> result?



AMBER mailing list
Received on Tue Nov 21 2017 - 05:30:02 PST
Custom Search