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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Received on Tue Oct 23 2018 - 15:30:03 PDT
