Shiho,
1, Installation
Did you follow the instructions in the Amber manual?
The installation process provided you with a descriptive error message
("nvcc cuda compiler not found"); maybe this is the point to start.
But others may provide more helpful comments...
2, Glycam
A glycam parameter set is available within Amber(Tools), please have a
look into the manual. (We did simulations with glycan-decorated proteins
in our group on GPUs without problems, as expected.)
If you want to incorporate special parameters, the normal rules for
external parameter usage in Amber apply (cf. the Amber manual).
Maybe this helps.
Regards,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
On 03/30/2022 08:24 AM, s.ohno.tohoku-mpu.ac.jp wrote:
> Dear Amber users,
>
>
>
> 1. I want to do a simulation using a GPU, so I am referring to the following
> method.
>
> http://ambermd.org/gpus12/
>
> I did this with reference to the Building and Testing the Default SPFP
> Precision Model section.
>
> ". /configure -cuda gnu" command, I got the following error code. Please let
> me know how to deal with this.
>
>
>
> Your AMBERHOME environment variable is not set! Auto set it to:
>
> /home/user/amber18
>
> Checking for updates...
>
> Checking for available patches online. This may take a few seconds...
>
>
>
> Available AmberTools 19 patches:
>
>
>
> No patches available
>
>
>
> Available Amber 18 patches:
>
>
>
> No patches available
>
>
>
>
>
> AMBER_PREFIX=/home/user/amber18
>
> AMBER_SOURCE=/home/user/amber18
>
>
>
> ./configure2: 1: python: not found
>
> Using the AmberTools miniconda installation in /home/user/amber18/miniconda
>
> version 2.7.16
>
> Error: nvcc cuda compiler not found in /usr/local/cuda-10.1/bin/
>
> Configure failed due to the errors above!
>
>
>
> 2. Also, I would like to incorporate the GLYCAM force field. Is there a
> specified directory to extract the GLYCAM.tgz file after obtaining it?
>
> 3. What page is the manual for incorporating the GLYCAM force field?
>
>
>
> Thank you in advance.
>
>
>
> Shiho ohno
>
>
>
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>
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Received on Wed Mar 30 2022 - 01:00:02 PDT
