I don't think that antechamber was used to prepare the inputs (or something
went wrong), because antechamber doesn't use upper case atom types.
As Dave Case said, you need to go through each step and look at your
outputs, then check the inputs for the next step. Something isn't getting
passed along correctly.
On Mon, Sep 9, 2019 at 12:26 PM RITUPARNA ROY <ritup176122023.iitg.ac.in>
wrote:
> The non-standard amino-acid which I am using is 2-amino benzoic acid.
> Using the mol2 files of the optimized structure of 2-amino benzoic acid,
> the atom types were generated using antechamber following the tutorial:
> http://ambermd.org/tutorials/basic/tutorial5/index.htm
> [http://ambermd.org/tutorials/basic/tutorial5/files/gfp_img.jpg1zB]<
> http://ambermd.org/tutorials/basic/tutorial5/index.htm>
> Amber Basic Tutorials - Tutorial A26<
> http://ambermd.org/tutorials/basic/tutorial5/index.htm>
> Introduction. This tutorial demonstrates how you would go about preparing
> a system with a modified amino acid in order to run a simulation using the
> AMBER molecular dynamics engines.
> ambermd.org
> After loading the prepi and frcmod files of 2-amino benzoic acid, I added
> it to a sequence of standard amino-acid residues and saved the pdb file.
> However. error rides while generating the parameter files.
>
>
> Rituparna Roy,
>
> Junior Research Fellow,
>
> Department of Chemistry,
>
> Indian Institute of Technology Guwahati.
>
> ________________________________
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sent: 09 September 2019 20:48
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Generating the parameters for non-standard amino-acid
> residue
>
> you'll need to give more information, as suggested by Dave Case. For
> example, how did you generate the atom types? The N2 type is for sp2 NH2
> groups, and should not occur in between 2 heavy atoms as shown in your
> torsion CX-C-N2-CA. The standard libraries probably do not have parameters
> for such a combination.
>
> On Mon, Sep 9, 2019 at 10:02 AM RITUPARNA ROY <ritup176122023.iitg.ac.in>
> wrote:
>
> > Sir,
> >
> > I am trying to replace an amino-acid residue with a non-standard
> > amino-acid in a short peptide fragment. After optimizing the structure of
> > this non-standard amino-acid, I did run parmchk2 to get the parameters
> and
> > also did load the frcmod file in tleap. I saved the pdb of the peptide
> > fragment with the replaced amino-acid residue, however, the atom name in
> > the pdb file doesn't match with the ones in the frcmod file, due to
> which,
> > I guess, the prmtop files are not getting generated. Kindly help.
> >
> >
> > Rituparna Roy,
> >
> > Junior Research Fellow,
> >
> > Department of Chemistry,
> >
> > Indian Institute of Technology Guwahati.
> >
> > ________________________________
> > From: David A Case <david.case.rutgers.edu>
> > Sent: 09 September 2019 18:20
> > To: AMBER Mailing List <amber.ambermd.org>
> > Subject: Re: [AMBER] Generating the parameters for non-standard
> amino-acid
> > residue
> >
> > On Sat, Sep 07, 2019, RITUPARNA ROY wrote:
> > >
> > >I am trying to generate the parameters for a peptide, consisting of a
> > >non-standard amino-acid. However. I'm getting the following error:
> > >
> > >/home/ritu/softwares/Amber/amber18/bin/teLeap: Error! ** No torsion
> terms
> > >for CX-C-N2-CA
> >
> > Unfortunately, you don't provide nearly enough information for anyone to
> > be able to help: how did you create the UNIT for the non-standard amino
> > acid? Did you run parmchk2 to get parameters? If so, does the frcmod
> > file you created have torsion terms like the one above (and the other
> > missing terms)? Did you remember to load this frcmod file in your tleap
> > run?
> >
> > ...etc
> >
> > ...dac
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
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> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Mon Sep 09 2019 - 10:30:02 PDT
