Hi all
Thank you for the help. I've come to realise when I swapped HIS to HIE to match residue names I was getting a single hydrogen that didn't match HIE lib file and did match HID. When I changed HIE to HID in the PDB file I was now getting other hydrogens, one per residue/multiple residues, that didn't match the HID lib file. I'm now working on the assumption that my enzyme has histidines both HID and HIE.
Is this common and is there a way of determining which HIS are HID or HIE without inspecting error messages and comparing PDB and lib files?
Thank you in advance
Sam
________________________________
From: Maria Nagan <maria.c.nagan.gmail.com>
Sent: 11 January 2021 17:37
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] LEaP Error/questions.
Hi Sam,
You want your pdb residue name to match the lib file name for the residue.
1) Here’s a link to the tutorial on building a protein system in explicit solvent:
https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fambermd.org%2Ftutorials%2Fbasic%2Ftutorial7%2Findex.php%23Protonation_states_&data=04%7C01%7CSam.Walsworth%40hud.ac.uk%7Cd6d48cafdb104aed879308d8b657c4d0%7Cb52e9fda06914585bdfc5ccae1ce1890%7C0%7C0%7C637459835382516237%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=n0nVzFUCDbO6%2FgNJeAhg3GxKJPlanjXFNVu2Gj2WYLQ%3D&reserved=0 <
https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fambermd.org%2Ftutorials%2Fbasic%2Ftutorial7%2Findex.php%23Protonation_states_&data=04%7C01%7CSam.Walsworth%40hud.ac.uk%7Cd6d48cafdb104aed879308d8b657c4d0%7Cb52e9fda06914585bdfc5ccae1ce1890%7C0%7C0%7C637459835382526229%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=vOtoMZRHNDXf0aRwrOH2kfBwKRu3PD6IaSWk1%2FdBWGA%3D&reserved=0>
Also, if you just have HIS, leap needs to know is it HIE or HID, etc. It defaults to making HIS —> HIE (specified at end of leaprc file).
2) In leap you loaded $AMBERHOME/dat/leap/cmd/oldff/leaprc.ff99SB, right? leaprc.ff99SB loads $AMBERHOME/dat/leap/lib/all_amino94.lib. Those are the amino acid residue names leap expects (those loaded from the lib file). Same issue with your NADH.lib file. The pdb name needs to match your NADH.lib.
Residue names are the same in ff19SB.
Maria
> On Jan 11, 2021, at 12:10 PM, Sam Walsworth (Researcher) <Sam.Walsworth.hud.ac.uk> wrote:
>
> Hi David
>
> I played around with the original PDB file and using pdb4amber and it mostly worked, except now I have HIE atoms not having a type (I believe I've seen issues regarding histidine protonation causing errors) and the NADH cofactor atoms types are not found. I'm using Ross Walker's contributed parameters for these ($AMBERHOME/dat/contrib/NADH_and_NAD+/NADH.lib) so I think I'm just missing a step in loading these into LEaP correctly.
>
> I'm using ff99SB because the simulations I'm recreating initially to learn how to deal with these enzyme-ligand complexes used it too. I have seen papers on ff14SB and ff19SB improving on ff99SB however
>
> Sam
> ________________________________
> From: David A Case <david.case.rutgers.edu>
> Sent: 11 January 2021 13:29
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] LEaP Error/questions.
>
> On Mon, Jan 11, 2021, Sam Walsworth (Researcher) wrote:
>>
>> When you load a complex into LEaP using complex = loadpdb ... does that pdb
>> file have to be all atoms or just the coordinates of the heavy non-hydrogen
>> atoms?
>
> It generally matters very little, since leap will add build in hydrogens in
> standard positions if they are missing.
>
>>
>> Also I got fatal errors saying atom does not have a type when I tried to
>> create parameters.
>
> You mention "complex": do you have a ligand or other non-standard component?
> Look at the "Developing non-standard parameters" at the tutorial tab on the
> Amber web page, especially tutorial 2.1 (if you have a ligand.)
>
> ...good luck...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=04%7C01%7CSam.Walsworth%40hud.ac.uk%7Cd6d48cafdb104aed879308d8b657c4d0%7Cb52e9fda06914585bdfc5ccae1ce1890%7C0%7C0%7C637459835382526229%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=jhIltRm5W%2FcIp%2BAKWboRx9psuK3TXHrcCUU6UXPAjVA%3D&reserved=0
> University of Huddersfield inspiring global professionals.
> [https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmarketing.hud.ac.uk%2F_HOSTED%2FEmailSig2014%2FEmailSigFooterMarch2019.jpg&data=04%7C01%7CSam.Walsworth%40hud.ac.uk%7Cd6d48cafdb104aed879308d8b657c4d0%7Cb52e9fda06914585bdfc5ccae1ce1890%7C0%7C0%7C637459835382526229%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=eA239ArwxdBEHKgDyWra46pjzzOa%2BZLFS8Q3lHAsODE%3D&reserved=0]
>
> This transmission is confidential and may be legally privileged. If you receive it in error, please notify us immediately by e-mail and remove it from your system. If the content of this e-mail does not relate to the business of the University of Huddersfield, then we do not endorse it and will accept no liability.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=04%7C01%7CSam.Walsworth%40hud.ac.uk%7Cd6d48cafdb104aed879308d8b657c4d0%7Cb52e9fda06914585bdfc5ccae1ce1890%7C0%7C0%7C637459835382526229%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=jhIltRm5W%2FcIp%2BAKWboRx9psuK3TXHrcCUU6UXPAjVA%3D&reserved=0
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=04%7C01%7CSam.Walsworth%40hud.ac.uk%7Cd6d48cafdb104aed879308d8b657c4d0%7Cb52e9fda06914585bdfc5ccae1ce1890%7C0%7C0%7C637459835382526229%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=jhIltRm5W%2FcIp%2BAKWboRx9psuK3TXHrcCUU6UXPAjVA%3D&reserved=0
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jan 11 2021 - 13:00:02 PST
