That makes sense, a mismatch in naming. Either way I've rebuilt everything from scratch and used LEaP to add hydrogens and it seems happy. I only persisted with MolProbity because the paper I'm working from used it too.
I did generate new NADH parms from R.E.DD.B project F-90 (also as per the paper) but it also gave me the same long bond issue so I'm not sure how the paper in question got theirs to work. Either way I think this has been solved (finally)
Thank you all
Sam
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________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Friday, January 15, 2021 8:41:17 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] LEaP Error/questions.
On Fri, Jan 15, 2021, Sam Walsworth (Researcher) wrote:
>I agree that the connections in NADH.lib look correct having tested
>them. I'm wondering if the hydrogens I'm adding (using MolProbity) are
>going to the wrong locations, hence the long bonds
Ah....molprobity will use the official naming scheme from the components.cif
library maintained by the wwPDB. Those standards did not exist two decades
ago, or whenever Ross made the library.
The *simplest* thing is just to not add hydrogens, either via molprobity or
by hand, and to remove any hydrogens that may be there already.
I don't know the "best" procedure for building a new NADH library: one would
want to take advantage of improvements in nucleic acid force fields, and
certainly to use standardized atom and residue nomenclature. You might
check out the libraries from Ulf Ryde at the contributed parameters
database:
https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fresearch.bmh.manchester.ac.uk%2Fbryce%2Famber&data=04%7C01%7CSam.Walsworth%40hud.ac.uk%7Ce112a3ccc3964b9382ce08d8b996319c%7Cb52e9fda06914585bdfc5ccae1ce1890%7C0%7C0%7C637463402458208440%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=SWfjEknSj%2F8o0oiev6nvxqxnzubXKPKr%2Fp%2FjOpAuw1g%3D&reserved=0
....dac
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Received on Fri Jan 15 2021 - 13:00:03 PST
