yes you can do this, but be aware that modifying amino acids can be tricky
since you want to make sure that the modified atom types match up to the
ones in your intended protein force field.
On Wed, Jul 17, 2024 at 2:13 PM SUBHASMITA MAHAPATRA MAHAPATRA via AMBER <
amber.ambermd.org> wrote:
> Thank you for your response.
>
> I would like to know if I could use antechamber for this purpose, as it
> uses the same am1-bcc method. I made a pdb with the serine and ligand
> combined. Then, run antechamber followed by parmchk2 to produce .frcmod
> files. I would like to know if this method is okay or if I should go for
> charge calculation separately.
>
> Kindly help in this regard.
>
> Thank you
>
> On Wed, Jul 17, 2024 at 4:04 PM Ghose Shouryo <Shouryo.Ghose.uliege.be>
> wrote:
>
> > Hello,
> >
> > You can user the Amber’s QUICK program to generate charges rather than
> > resp say am1 or bcc. This does not require Gaussian..
> >
> > Best
> >
> > Shouryo
> >
> >
> >
> > *From: *SUBHASMITA MAHAPATRA MAHAPATRA via AMBER <amber.ambermd.org>
> > *Date: *Wednesday, 17 July 2024 at 12:32
> > *To: *AMBER Mailing List <amber.ambermd.org>
> > *Subject: *[AMBER] running tleap for complex having covalent bond between
> > protein and ligand
> >
> > Hi,
> >
> > I am running tleap for a complex pdb with a covalent bond between SER46
> of
> > protein and CAH atom of ligand. I am following this tutorial:
> > https://ambermd.org/tutorials/advanced/tutorial1_adv/. However, I am
> stuck
> > with the RESP charge calculation as I don't have a license for Gaussian.
> > Also, I would like to know how to generate the .frcmod file.
> >
> > Kindly help me in this regard.
> >
> > Thank you
> >
> > --
> > *Yours Sincerely*
> > *Subhasmita Mahapatra*
> > *Ph.D. Scholar (PMRF)*
> > *Computational Biophysics Group*
> > *Department of Biosciences and Biomedical Engineering*
> > *Indian Institute of Technology, Indore*
> > *Madhya Pradesh, India (453552)*
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> *Yours Sincerely*
> *Subhasmita Mahapatra*
> *Ph.D. Scholar (PMRF)*
> *Computational Biophysics Group*
> *Department of Biosciences and Biomedical Engineering*
> *Indian Institute of Technology, Indore*
> *Madhya Pradesh, India (453552)*
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jul 17 2024 - 11:30:03 PDT
