Hi,
>
> > MPI = loadpdb mpi_noligand.pdb
> Warning: Unknown residue: Zn2....
> ..relaxing end constraints to find a dbase match
>
Just to add on, it might be a formatting/name problem- I've had issues with
4 letter resnames in leap where I think it truncates the name down to just
3 letters, so when you have Zn2+ it might be reading it as a Zn2, minus the
+. Not sure if that's what it's actually doing, but that was my
interpetation.
There might be an actual solution, but I've gotten around it by just
renaming it to 2-3 letters, ie you can change the Zn2+ in the frcmod file
to Zn2 if Maria's solution hasn't fixed it.
Best,
Kenneth
On Fri, Feb 12, 2021 at 5:15 PM Maria Nagan <maria.c.nagan.gmail.com> wrote:
> 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
> >>
> >> 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%7C8560aad5856341b6139e08d8cf9fb601%7Cb52e9fda06914585bdfc5ccae1ce1890%7C0%7C0%7C637487632147624258%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=Td5XOa%2Beiti6AuOH1PybRvz57DYCUFqc4FpOTwT%2BRVM%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%7C8560aad5856341b6139e08d8cf9fb601%7Cb52e9fda06914585bdfc5ccae1ce1890%7C0%7C0%7C637487632147624258%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=hizla2OYeDhrcftG9EnXST4WmPK6pofaaWrsqZvzCaA%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%7C8560aad5856341b6139e08d8cf9fb601%7Cb52e9fda06914585bdfc5ccae1ce1890%7C0%7C0%7C637487632147624258%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=hizla2OYeDhrcftG9EnXST4WmPK6pofaaWrsqZvzCaA%3D&reserved=0
> > _______________________________________________
> > 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
>
--
Ask yourselves, all of you, what power would hell have if those imprisoned
here could not dream of heaven?
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 12 2021 - 14:30:04 PST
