Sam,
>
> I can't find a .lib file that contains Zn2+, only a series of .frcmod files that do.
grep ZN * in $AMBERHOME/dat/leap/lib folder found:
$AMBERHOME/dat/leap/lib/atomic_ions.lib
Also Yuan-Ping Pang parameters:
https://www.mayo.edu/research/labs/computer-aided-molecular-design/projects/zinc-protein-simulations-using-cationic-dummy-atom-cada-approach
found on Force Fields tab on ambermd.org
Maria
>
>
>
>
> ________________________________
> From: Maria Nagan <maria.c.nagan.gmail.com>
> Sent: 12 February 2021 21:45
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Using divalent ions in LEaP
>
> Dear Sam,
>
> You need the exact name in your pdb file to match the name in the lib file and frcmod file.
>
> The general order is to:
> load lib files for all your molecules (e.g. protein, ions, water)
> This tells Amber what your residues names, atoms, etc. are called and your charges
> load frcmod files for all your molecules (e.g. protein, ions, water)
> This tells Amber what your atom types, force constants, etc. are called
> load your pdb file
> Parameters are listed on the Amber website under “Force Fields”
> https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fambermd.org%2FAmberModels.php&data=04%7C01%7CSam.Walsworth%40hud.ac.uk%7C8560aad5856341b6139e08d8cf9fb601%7Cb52e9fda06914585bdfc5ccae1ce1890%7C0%7C0%7C637487632147624258%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=KCm34gev0fWfT4sgDwTeT%2BYDz%2FoFUbyBau38CtiKlcc%3D&reserved=0
>
> lib files can be also found under:
> $AMBERHOME/dat/leap/lib
>
> frcmod files can be also found under:
> $AMBERHOME/dat/leap/parm
>
> You should make sure your pdb file residue names match your lib file residue names. You are missing Zn2+ cation parameters.
>
> Maria
>
>> On Feb 12, 2021, at 4:30 PM, Sam Walsworth (Researcher) <Sam.Walsworth.hud.ac.uk> wrote:
>>
>> Hello all
>>
>> I'm trying to run simulations of a protein that has a zinc 2+ cofactor. The amber manual mentions you can use relevant frcmod files for di/tri/tetravalent ions (e.g. frcmod.ions234lm_126_tip3p has Zn2+ parameters to be used with tip3p, the frcmod file I'm interested in). The problem is LEaP doesn't recognise the Zn2+ species in my pdb file (for some reason the + in Zn2+ seems to be omitted when read from a PDB file so I called my zinc ion Zn2 in the PDB and renamed the Zn2+ in the frcmod to Zn2 to try make them match):
>>
>>> MPI = loadpdb mpi_noligand.pdb
>> Warning: Unknown residue: Zn2....
>> ..relaxing end constraints to find a dbase match
>>
>> Warning: -no luck
>>
>> # Proceeds to create Zn residue, so I tried to load in the frcmod in question
>>
>>> loadamberparams frcmod.ions234lm_126_tip3p
>> Loading parameters: ./frcmod.ions234lm_126_tip3p
>> .
>> .
>>> check MPI
>> .
>> FATAL : Atom .R<Zn2 442>.A<Zn2 1> does not have a type.
>>
>> I'm not sure if I'm misunderstanding the amber manual and I'm trying to load the wrong file (or that I need to load an additional file) or if I'm simply getting something more basic wrong like formatting/doing things in the wrong order etc.
>>
>> Thanks in advance
>> Sam
>>
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Received on Fri Feb 12 2021 - 14:30:03 PST
