Hi Pengfei,
Thank you for clearing this up.
Perhaps opening up the actual scientific dilemma behind my enquiry might prove fruitful.
I'm attempting to parameterise 4 calcium ions and 2 zinc ions in a metalloprotease. The last time I parameterised metal for a protein was quite a few years ago and I did it by writing my own 2nd derivative of the Hessian-based model using a Gaussian log file. Unfortunately, I don't have access to a Gaussian license anymore. I've requested a GAMESS-US license, but I've never used that before.
Are there any empirical calculations I can perform to derive force constants? To satisfy charges I believe I can still use the RED server.
Thanks
Anthony
Kind regards
Dr Anthony Nash PhD MRSC
Senior Research Scientist
Nuffield Department of Clinical Neurosciences
RMCR Kellogg College
University of Oxford
http://www.kellogg.ox.ac.uk/
________________________________
From: Pengfei Li <ambermailpengfei.gmail.com>
Sent: 21 July 2021 03:29
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Missing mtkpp directory after installation of AmberTools21
Hi Anthony,
As Dave said, the new version of AmberTools does not have MCPB in it.
MCPB.py has a different usage from MCPB, which means it does not need the genMetalFF.sh script anymore.
Here are two tutorials for MCPB.py: https://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.php <https://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.php>, https://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.php <https://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.php>.
Hope it helps,
Pengfei
> On Jul 20, 2021, at 9:55 AM, Anthony Nash <anthony.nash.ndcn.ox.ac.uk> wrote:
>
> In answer to my own question, I created a new environment and I've downloaded and installed AmberTools21 from source.
>
> However, having now looked through the manual pdf, and compared it to the HTML page dating 2015 which begins with running genMetalFF.sh, all of the required variables for MCPB.py aren't in the bcl files that genMetalFF originally generated.
>
> Rather than hack around hoping something will work, is there a latest and greater bonded model tutorial specifically designed with the latest MCPB.py in mind?
>
> Thanks
> Anthony
>
> Kind regards
> Dr Anthony Nash PhD MRSC
>
> Senior Research Scientist
> Nuffield Department of Clinical Neurosciences
> RMCR Kellogg College
> University of Oxford
> http://www.kellogg.ox.ac.uk/
>
> ________________________________
> From: Anthony Nash <anthony.nash.ndcn.ox.ac.uk>
> Sent: 19 July 2021 14:37
> To: amber.ambermd.org <amber.ambermd.org>
> Subject: Missing mtkpp directory after installation of AmberTools21
>
> Dear all,
>
> I'm a new user of AMBER but a long time MD modeller and I'm hoping I can get some help resolving a post-installation concern over what and where some of the files are.
>
> I am trying to step through the bonded metal-binding centre tutorials given here: https://ambermd.org/tutorials/advanced/tutorial20/mcpb.php
>
> The only difference is that I'm using my own set of pdb files. Six in total; two zinc-based and four calcium-based coordination centres.
>
> I installed AmberTools21 in Linux (in fact, it was WSL2 Ubuntu) using conda. The installation didn't flag up any problems.
>
> These are my concerns/issues:
>
> Firstly, as per the tutorial linked above, I wasn't able to find genMetalFF.sh in my AMBERHOME directory structure. So, I downloaded the file from the link provided in the tutorial and generated the corresponding setup files for MCPB.
>
> Then, the next slight concern I ran into was upon investigating zinc_1201_settings.bcl (one of my generated files) I noticed the directory structure AMBERHOME/dat/mtkpp/ is missing!
>
> Finally, before resorting to this email, I was unable to find the MCPB executable. Instead, I'm able to find MCPB.py (of which, I've noticed the command line arguments are slightly different to the command line arguments of MCP B). Either way, I decided to execute the python executable and I got the following error:
>
> Traceback (most recent call last):
> File "/home/ubuntu/miniconda3/envs/AmberTools21/bin/MCPB.py", line 67, in <module>
> options.step = options.step.lower()
> AttributeError: 'NoneType' object has no attribute 'lower'
>
>
> All suggestions are welcome.
>
> Many thanks
> Anthony
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 21 2021 - 06:30:02 PDT
