Hello
I am thankful for your suggestion and for the information that you have
provided.
Currently, I was tying to make the required library file for the Gamma
glutamic acid (unusual amino acid) using xleap by following the tutorial :
http://ambermd.org/tutorials/advanced/tutorial1_orig/ . After loading the
constructed .lib in addition to the amber force field parameters,
fortunately the gamma linkages were constructed as per requirement.
However, when saving the prmtop and incrd file an error is occurring. xleap
is creating additional terminal hydrogen molecules for the free NH2 group
on the alpha carbon of glutamic acid and thereafter giving the following
error message.
saveamberparm mol protein.prmtop protein.inpcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: -3.990000 is not zero.
WARNING: The perturbed charge: -3.990000 is not zero.
FATAL: Atom .R<GGL 1>.A< 3> does not have a type.
FATAL: Atom .R<GGL 1>.A<H2 19> does not have a type.
FATAL: Atom .R<GGL 4>.A< 3> does not have a type.
FATAL: Atom .R<GGL 4>.A<H2 19> does not have a type.
FATAL: Atom .R<GGL 7>.A< 3> does not have a type.
FATAL: Atom .R<GGL 7>.A<H2 19> does not have a type.
Failed to generate parameters
Parameter file was not saved.
If anyone could help me proceed, it would be very helpful. Please suggest
if I can remove the h2 atoms which xleap created as following:
Created a new atom named: H2 within residue: .R<GGL 1>
Created a new atom named: H2 within residue: .R<GGL 4>
Created a new atom named: H2 within residue: .R<GGL 7>
Thank you
with regards
Rajbinder Kaur Virk
On Wed, Oct 24, 2018 at 3:57 AM Matias Machado <mmachado.pasteur.edu.uy>
wrote:
> Dear Rajbinder,
>
> > There is an unusual amino acid in the protein, gamma-carboxyglutamic
> acid,
> > to which leap program is adding the missing terminal OXT group and
> breaking
> > its peptide linkage to other amino acids while building the missing
> hydrogen molecules.
>
> 1) Where do the topology for gamma-carboxyglutamic acid come from? Because
> there may be an implementation issue in the custom libraries or prep files
> that you are using... you need to define the unit connector atoms in order
> to link this residue to others in the chain
>
> > I am quite new to this field, please pardon me for any mistake, I
> > wanted to inquire a) if we could build the parameter and force field
> > file for gamma-carboxyglutamic as given for the charmm force field
> >
> https://www.ks.uiuc.edu/Training/Tutorials/science/topology/topology-tutorial.pdf
> > b) or if we can source charmm force field in leap
> > c) or if we can follow the scheme of using antechamber and parmcheck2
> > to generate the necessary files.
>
> 2) I don't know which force field you are using, but mixing force field
> it's a very bad idea... each force field was derived considering a
> particular Hamiltonian of a particular functional form with particular
> extra terms (e.g. CMAP in CHARMM), for particular Lennard-Jones
> combinations rules, with specific 1-4 scaling factors, using specific
> fitting methods to derive charge from a given level of theory, and
> everything was meant to run on particular water model... So it isn't true
> that you can swap residue parameters from one force field to another, they
> just mean different things... the same goes for parametrization
> protocols... so you either do the parameterization in CHARMM, transform the
> full topology into AMBER format by using Parmed and then run CHARMM on
> AMBER... or you stick in AMBER all the time running AMBER on AMBER...
>
> Best,
>
> MatÃas
>
> ------------------------------------
> PhD.
> Researcher at Biomolecular Simulations Lab.
> Institut Pasteur de Montevideo | Uruguay
> [http://pasteur.uy/en/laboratorios-eng/lsbm]
> [http://www.sirahff.com]
>
> ----- Mensaje original -----
> De: "Rajbinder Kaur Virk" <rajbinderkaurvirk.gmail.com>
> Para: amber.ambermd.org
> Enviados: Lunes, 22 de Octubre 2018 0:06:30
> Asunto: [AMBER] tleap gamma-carboxyglutamic acid linkage error
>
> Hello
> We were trying to use mcpb program of amber, in order to generate
> force field parameters of a metaloprotein complex. After reaching the
> final step, leap program was initiated. There is an unusual amino acid
> in the protein, gamma-carboxyglutamic acid, to which leap program is
> adding the missing terminal OXT group and breaking its peptide linkage
> to other amino acids while building the missing hydrogen molecules.
> I am quite new to this field, please pardon me for any mistake, I
> wanted to inquire a) if we could build the parameter and force field
> file for gamma-carboxyglutamic as given for the charmm force field
>
> https://www.ks.uiuc.edu/Training/Tutorials/science/topology/topology-tutorial.pdf
> b) or if we can source charmm force field in leap
> c) or if we can follow the scheme of using antechamber and parmcheck2
> to generate the necessary files.
> Further, we intend to use the sander program of amber.
> Eagerly looking forward for suggestions
> Thank you
> With regards
> Rajbinder Kaur Virk
>
> --
> *With regards*
>
> *Rajbinder Kaur Virk*
> *Research Scholar *
> *Department of Biophysics*
> *Panjab University *
> *Chandigarh-160014*
>
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--
*With regards*
*Rajbinder Kaur Virk*
*Research Scholar *
*Department of Biophysics*
*Panjab University *
*Chandigarh-160014*
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Received on Wed Oct 24 2018 - 23:00:02 PDT
