Hello
I am grateful for the information, by comparing files , this error was
eliminated. Thereafter, pdb, prmtop and inpcrd file was saved with the help
of xleap. I checked the pdb file and gamma linkages were successfully
present. When, these prmtop and inpcrd files were used to perform molecular
dynamic by sander unit of amber, the trajectories files had no gamma
linkage i.e no peptide bond was present. Thus again in xleap, I tried to
use the bond command to generate the necessary file, I have done many
attempts but failing every time.
one of the errors was:
Could not find angle parameter: O2 - C - N
Warning: No sp2 improper torsion term for CT-O2-C-N
atoms are: CA OXT C N
thereafter i tried to provide the required parameters in the .dat file
itself (frcmod.ff14SB), still the parameter are not being recognized and
the error persists.
Suggestions will be very much appreciated.
Thank you
with regards
Rajbinder Kaur Virk
On Sat, Oct 27, 2018 at 12:16 AM Matias Machado <mmachado.pasteur.edu.uy>
wrote:
> Dear Rajbinder,
>
> The messages:
>
> Created a new atom named: H2 within residue: .R<GGL 1>
> FATAL: Atom .R<GGL 1>.A<H2 19> does not have a type.
>
> imply a naming inconsistency in GGL between the residue library and the
> PDB file you are loading into leap... all atoms must match in both files
>
> This other message points to an atom name "" or " " at the library or PDB:
> FATAL: Atom .R<GGL 1>.A< 3> does not have a type.
>
> Best,
>
> Matias
>
> ----- Mensaje original -----
> De: "Rajbinder Kaur Virk" <rajbinderkaurvirk.gmail.com>
> Para: amber.ambermd.org
> Enviados: Jueves, 25 de Octubre 2018 2:39:03
> Asunto: Re: [AMBER] tleap gamma-carboxyglutamic acid linkage error
>
> 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*
> >
> > _______________________________________________
> > 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
> >
>
>
> --
> *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 Tue Oct 30 2018 - 10:30:02 PDT
