when building a system in leap, you can either load the pdb, or specify the
sequence if you don't have a structure (technically you can do both, but
that's advanced).
if you have a pdb file, try replacing the "peptide = sequence" command with
"peptide = loadpdb xx.pdb" where xx.pdb is your pdb file name.
On Thu, Nov 18, 2021 at 3:27 PM Yen Nguyen <ynguyen3.gmu.edu> wrote:
> Hi Carlos,
>
> Thank you so much for the quick response. I just want to clarify if what I
> understand is right.
>
> So to build my modified peptide sequence in tleap, I'd type the following
> command (AA stands for amino acid)
> peptide = sequence {ACE TRP AA2 AA3 ... LYS NHE } ?
>
> The ACE TRP would give me acetylated Trp on the N-terminal and LYS NHE
> would give me amidated Lys on the C-terminal? Is that correct?
>
> I forgot to mention that I'm doing a peptide simulation using the
> guidelines from this tutorial on AMBER
> https://ambermd.org/tutorials/basic/tutorial0/index.php#Solvate_alanine_dipeptide
> Simple Simulation of Alanine Dipeptide - AMBER<
> https://ambermd.org/tutorials/basic/tutorial0/index.php#Solvate_alanine_dipeptide
> >
> In order to run a molecular dynamics simulation, we need to load a force
> field to describe the potential energy of alanine dipeptide. We will use
> the AMBER force field FF19SB1 for proteins. To learn more about force
> fields, please look through section 3.1.1 on page 36 of the Amber 2020
> Manual.. 5.
> ambermd.org
> I don't really see where my pdb file could be used in the entire process.
> But I'm wondering if I could use the command peptide = loadpdb "my peptide
> pdb file" to use it for the next steps in the tutorial, e.g. solvation,
> creating prmtop and rst files, etc.
>
> Thank you.
>
> Yen Nguyen
> Graduate Research Assistant
> George Mason University
> Department of Chemistry and Biochemistry
> ________________________________
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sent: Thursday, November 18, 2021 2:55 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] How to add an amidated residue at the C-terminal in
> AMBER tleap ?
>
> I think you're looking for the "NHE" residue.
> it should work ok if your pdb file has the matching residue and atom names.
> if not, you can rename them following the info below:
>
> NHE INT 1
> NH2 ENDING GROUP
> 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300
> 5 HN1 H E 4 3 2 1.010 119.800 0.000 0.23150
> 6 HN2 H E 4 3 2 1.010 119.800 180.000 0.23150
>
> On Thu, Nov 18, 2021 at 2:48 PM Yen Nguyen <ynguyen3.gmu.edu> wrote:
>
> > Hello,
> > I've been searching for a way to build a peptide sequence with C and N
> > terminal modifications (C -terminal = amidated Lys, N-terminal =
> acetylated
> > Trp in tleap (AMBER), but I couldn't find a way to make/add an amidated
> Lys
> > residue at the C-terminal. AMBER has the code ACE for acetylated
> residues,
> > but I don't know if it has a code for amide terminals?
> > I'm using amber 18 and the protein forcefield leaprc.protein.ff14SBonlysc
> > , which has the following parameter files
> > /amber20/dat/leap/parm/parm10.dat
> > frcmod.ff14SB
> > frcmod.ff99SB14
> > I have a pdb file of the peptide, but it looks like AMBER doesn't utilize
> > pdb files to create prmtop and coordinate files for my peptide.
> > I'd greatly appreciate any help. Thank you!
> >
> > Yen Nguyen
> > Graduate Research Assistant
> > George Mason University
> > Department of Chemistry and Biochemistry
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> >
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Received on Thu Nov 18 2021 - 13:00:02 PST
