Hello Carlos,
When I tried to load my pdb file in tleap and run it, the final structure is wrong.
So I tried building the structure from scratch in tleap using the following command
AbSOD-15aa-modified = sequence { ACE TRP GLU HID ALA TYR TYR ILE ASP PHE ARG ASN LEU ARG PRO LYS NHE}
and the output structure is correct when I viewed it in chimera.
But when I tried to save the parm7 and rst7 files after solvating the peptide, I got these messages.
saveamberparm AbSOD-15aa-modified parm7 rst7
Checking Unit.
Warning: The unperturbed charge of the unit (1.000000) is not zero.
Note: Ignoring the warnings from Unit Checking.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 73 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
ACE 1
NHE 1
)
(no restraints)
Should I fix the charge of the system so it is 0 before doing anything else? Like try adding Cl- ion to neutralize it?
I also don't know if the ACE 1 and NHE1 not being recognized is going to cause a big problem in the simulation.
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 3:33 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] How to add an amidated residue at the C-terminal in AMBER tleap ?
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://secure-web.cisco.com/1iV0T-fHKHEmJqsLjwxLmkiQDG9bolcox6e78L2Pw29UsoCaEbjT6Qx1hrl0rY7vZxmyOx4qbfnJLrai_el2SaAjmb0OXgmVC1a6UOmhAAqwb1RUerOSmZCGOgX-ES4NfWzqmXhe3qHLR6n6EQnLtK-jRu_uPpYY-GlshJaEVe6SU6cwx8Dnn5AqF7JGWh2sZOhZOsWjL-iXYiO6X0YuhL72kr4ywxG9vHUke2ZFjHoSYgiD1qvRY1Ai2-iKwDCqvHgUVYAm1WP2ZjNDd3yF01ZibBMylLar6qVEz8eCCDTAZ-BasBM3lG_Kj7A9dHt2LwDi27JYYphuXKI3K9A_05A1TQlSZlDDnsO0kL0gXCqyGmkA2Waeo4u6YAxfW6cT94D3pPRFuyfEt-_K3Id0uQhgCgorPbBp3OUfBf_sSnhoY3RLb-KgrtXr5iqvmCh-h/https%3A%2F%2Fambermd.org%2Ftutorials%2Fbasic%2Ftutorial0%2Findex.php%23Solvate_alanine_dipeptide
> Simple Simulation of Alanine Dipeptide - AMBER<
> https://secure-web.cisco.com/1iV0T-fHKHEmJqsLjwxLmkiQDG9bolcox6e78L2Pw29UsoCaEbjT6Qx1hrl0rY7vZxmyOx4qbfnJLrai_el2SaAjmb0OXgmVC1a6UOmhAAqwb1RUerOSmZCGOgX-ES4NfWzqmXhe3qHLR6n6EQnLtK-jRu_uPpYY-GlshJaEVe6SU6cwx8Dnn5AqF7JGWh2sZOhZOsWjL-iXYiO6X0YuhL72kr4ywxG9vHUke2ZFjHoSYgiD1qvRY1Ai2-iKwDCqvHgUVYAm1WP2ZjNDd3yF01ZibBMylLar6qVEz8eCCDTAZ-BasBM3lG_Kj7A9dHt2LwDi27JYYphuXKI3K9A_05A1TQlSZlDDnsO0kL0gXCqyGmkA2Waeo4u6YAxfW6cT94D3pPRFuyfEt-_K3Id0uQhgCgorPbBp3OUfBf_sSnhoY3RLb-KgrtXr5iqvmCh-h/https%3A%2F%2Fambermd.org%2Ftutorials%2Fbasic%2Ftutorial0%2Findex.php%23Solvate_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 Mon Dec 13 2021 - 11:00:02 PST
