Hello
I am grateful for the generous help of AMBER users, with your help
and support my problem has been solved, the gamma linkage of the unusual
amino acid, gamma glutamic acid has been established.
As suggested the errors were the following:
C terminal (head) and N terminal (tail) were defined in the constructed
library file, however it had to be changed as now the c terminal was the
carboxyl group of the side chain.
Also atom types had to be changed.
Thereafter, proper linkages were formed while using the ff14SB parameters.
Thank you for your time
with regards
Rajbinder Kaur Virk
On Wed, Oct 31, 2018 at 10:57 PM Matias Machado <mmachado.pasteur.edu.uy>
wrote:
> Dear Rajbinder,
>
> As David and Bill said there is no need to modify frcmod.ff14SB to add new
> (or missing) parameters to the force field. I recommend you to see how
> FFPTM is implemented on AMBER [http://selene.princeton.edu/FFPTM]
>
> In practical terms I'd use this kind of leap input file:
>
> # Load AMBER force field
> source leaprc.protein.ff14SB
>
> # Load custom parameters
> loadOff gamma-coo-GLU.lib
> loadAmberParams gamma-coo-GLU.frcmod
>
>
> Where gamma-coo-GLU.lib is the library containing the residue topology, it
> can also be a prep file, in which case the command is "loadAmberPrep
> gamma-coo-GLU.prep"...
>
> gamma-coo-GLU.frcmod is the parameter file containing the following
> sections [http://ambermd.org/FileFormats.php#frcmod]:
>
> remark goes here
>
> ANGLE
> O2-C -N 72.7 120.63
>
> IMPR
> CT-O2-C-N 10.5 180. 2.
>
> In that way you are sure to preserve the original ff14SB parameters
>
> Something I can't understand is the way you are linking the
> gamma-carboxyglutamic acid to other amino acids in the chain... it seems
> you are joining the OXT (carboxylic group of the side chain) to the peptide
> backbone of the next residue instead of joining the peptide backbones...
> that seems rare to me but I know anything about your system... Any way, as
> I mentioned in a mail before, the .lib format allows you to set the head
> and tail linking atom, so the bonds in residue chains can be generated
> automatically without the need for a bond command see the documentation at
> AMBER web page [http://ambermd.org/doc/OFF_file_format.txt]... I guess
> you can set kind of similar things in prep files but I'm not used to use
> them...
>
> Best,
>
> Matias
>
> ----- Mensaje original -----
> De: "Bill Ross" <ross.cgl.ucsf.edu>
> Para: amber.ambermd.org
> Enviados: Miércoles, 31 de Octubre 2018 6:30:25
> Asunto: Re: [AMBER] tleap gamma-carboxyglutamic acid linkage error
>
> Coming on this cold with a Sherlock Holmes approach and vestigial
> awareness of chemistry (i.e. Dave's issue and your response), an obvious
> possibility is that the frcmod.ff14SB file you added the params to is
> not the one you are loading. Try listing the param in leap, or some
> addition or deletion experiment to prove to yourself that you are
> loading the right file, then burn this message and fly into the night. :-)
>
> Bill
>
>
> On 10/31/18 2:13 AM, Rajbinder Kaur Virk wrote:
> > Hello
> >
> > This missing parameters is probably due the presence of gamma glutamic
> acid
> > as one of the amino acid in the peptide and it is forming a gamma linkage
> > as peptide bond. As discussed earlier, I tried to make .lib file, after
> > saving by xleap, the pdb seems to be right but prmtop and inpcrd files
> are
> > not being saved.
> >
> > Following changes were made in the frcmod.ff14SB file:
> > Angle
> > O2-C -N 72.7 120.63
> > IMPR
> > CT-O2-C-N 10.5 180. 2.
> >
> > Please provide some suggestions....we are really stuck. Thank you
> >
> > Thank you
> > With regards
> > Rajbinder Kaur Virk
> >
> >
> > On Wed, Oct 31, 2018 at 7:11 AM David Case <david.case.rutgers.edu>
> wrote:
> >
> >> On Tue, Oct 30, 2018, Rajbinder Kaur Virk wrote:
> >>> Could not find angle parameter: O2 - 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.
> >> Can you show the exact changes to the frcmod.ff14SB file you made, plus
> all
> >> the commands you gave to tleap?
> >>
> >> As an aside, you should generally not edit frcmod.ff14SB itself, but
> rather
> >> make a new frcmod file--that way you won't mess up other runs that
> expect
> >> to
> >> have the un-modified frcmod.ff14SB file.
> >>
> >> Second aside: there are indeed no O2-C-N angles in ordinary proteins.
> Are
> >> you
> >> sure you have correct atom types?
> >>
> >> ....dac
> >>
> >>
> >> _______________________________________________
> >> 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
>
> _______________________________________________
> 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*
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Nov 03 2018 - 01:30:03 PDT
