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

From: Amit Sharma (Asstt. Prof., MCARS) <"Amit>
Date: Wed, 4 Nov 2020 21:52:54 +0530

Thank You David,

Can you also guide about how to generate .lib or .mol2 file for CFN because
CFN is a non standard cysteine residue.

CFN is built through a covalent bond bstween SG of CYM (cysteine with non
reducable SG) and C4A carbon of flavin mononucleotide (FMN). Amber could
help generate lib or mol2 files for FMN because its FMN.cif is available in
pdb database. But, how to deal with CFN (or how to get its .cif) is giving
tough time to me.



On Wed, 4 Nov 2020, 18:46 David A Case, <> wrote:

> On Wed, Nov 04, 2020, Amit Sharma (Asstt. Prof., MCARS) wrote:
> >
> >> source leaprc.protein.ff14SB
> >> source leaprc.gaff
> >> com = loadpdb CFN.pdb
> >> chig = sequence { ACE com NME }
> Above is incomplete. You need to load the CFN residue by using a command
> like "loadOff CFN.lib" or "CFN = loadMol2 CFN.mol2" After one of these
> commands, type "list" to be sure that you have a CFN unit loaded, and
> use the "desc" command to look at what is inside it, especially at the
> head and tail properties. Compare the description of CFN to what you
> get for ALA (say), to see what an amino acid unit is supposed to look
> like.
> Then your sequence command would look like "sequence { ACE CFN NME }"
> ...hope this helps....dac
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Received on Wed Nov 04 2020 - 08:30:02 PST
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