Re: [AMBER] Help with parameterization of non-standard amino acid

From: Amit Sharma (Asstt. Prof., MCARS) <"Amit>
Date: Wed, 4 Nov 2020 15:00:31 +0530

Dear Anselm,

Kindly let me know how can I add ACE and NME to the nonstandard residue

I have tried (with no success) the following in tleap

> source leaprc.protein.ff14SB
> source leaprc.gaff
> com = loadpdb CFN.pdb
> chig = sequence { ACE com NME }
This gives
Warning: One sided connection. Residue (default_name) missing connect0 atom.

Warning: One sided connection. Residue (ACE) missing connect1 atom

and on saving chig as
> savepdb chig aceCFNnme.pdb

ACE and NME does not get connected to CFN



On Wed, Oct 28, 2020 at 8:30 PM Dr. Anselm Horn <> wrote:

> Hi Amit,
> maybe your parameterization approach is not right.
> You need parameters for a modified Cys residue, thus you may want to use
> a model peptide for parameterization like ACE-CFN-NME.
> For this model peptide, you can derive atomic charges (for one or more
> conformations), e.g. via the R.E.D./PyRed server.
> Then you have to decide, which forcefield parameter set to use for your
> protein system and thus for your CFN. After assigning the atom types for
> all atoms in your residue, you may find that some of the necessary
> parameters are missing. For those, parameters are to be generated either
> by separate computations or by adaption from existing force fields.
> There are tutorials on the Amber website about how to parameterize
> non-standard amino acids.
> Regarding your question, whether you can re-use CFN parameters from
> Gromacs for Amber: It depends.
> Gromacs and Amber are the program suits. If the published Gromacs
> parameters were created for the forcefield you intend to use in Amber,
> you can savely use those. If they are for a different force field, they
> may merely be used as hint.
> Regards,
> Anselm
> > I am trying to parameterize (get .top and .rst7 files) a protein molecule
> > with a non standard amino acid cysteinyl-flavin (CFN). CFN contains a
> > covalent bond between C4A of flavin mononucleotide (FMN) and SG of
> > Cysteine.
> >
> > I tried antechamber with no success perhaps due to the following reasons
> >
> > 1. pdb4amber or reduce is not adding hydrogens to CFN. Although reducing
> > other residues in the protein
> > 2. cif file is not available for CFN. Although, the cif file is available
> > for FMN. So parametrization with antechamber works if I treat CYS (as CYM
> > (to not reduce SG)) and FMN as separate in the protein pdb. But, doing so
> > breaks the cysteine- FMN covalent bond during minimization. I want to
> > retain this bond intact during the simulation. Therefore trying to
> > parametrize the protein molecule in which CYS and FMN are treated as one
> > residue CYM.
> >
> > I have also tried restraining CYM and FMN using strong force constants on
> > these two, but covalent bond breaks during minimization.
> >
> > After trying these options I write here to seek help with creating
> > parameter files for the protein containing CFN residue in AMBER.
> >
> > Also, like to mention here that parameters for CFN are built and
> published
> > using GROMACS. Can we use these or modify these to work in amber?
> >
> > Thank You,
> >
> > Amit
> >
> _______________________________________________
> AMBER mailing list

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Received on Wed Nov 04 2020 - 02:00:02 PST
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