On Fri, May 16, 2014, berin karaman wrote:
>
> I am trying to simulate a 7 residue peptide with acetylated lysine =
> TARKacSTG (peptide-full.pdb)
>
>
> First, I generated the prep file (ACK-ac-ext.prep) for acetylated
> lysine part using antechamber with an extended molecule including
> acetylated lysine (ACK-ac-extended.mol2). Then with parmcheck I
> generated frcmod file. (ACK-ac-ext.frcmod).
>
> In xleap, I deleted the extended part of the acetylated lysine
> molecule and then put the right charges for each atom as stated
> in one paper.
At this point, I would recommend that you re-save the updated lysine-only
mol2 file (to a new filename, for safety). That way, you can use it later on
for any peptide with a modified lysine residue.
Next, create a complete pdb file with all the residues (you might have some
missing atoms near the lysine modification. Make sure the lysine residue has
the same residue name as in your mol2 file.
In LEaP, load the new mol2 file, the frcmod file, then use loadPdb to load
the peptide pdb file. If things work, you can now continue, say with
saveAmberParm, etc.
> There is no error when I re-opened the peptide.However, I realise that
> amber converts the two ending of the peptide as in proteins. And for
> the -NH2 group in T residue it becomes as the -NH3 and amber assigns it
> like N-terminus and for the H-CO group in G residue H becomes OXT and
> amber assigns it like C-terminus
Is this not the behavior that you want? What sorts of terminii would you like
to have on the peptide? This can be controlled by editing your leaprc file,
but the default behavior is certainly what would be expected in solution,
which is the environment for which the Amber force fields have been developed.
....dac
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Received on Fri May 16 2014 - 05:30:03 PDT
