Dear Amber Users,
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. Then I imported the rest of the peptide residues (peptide-rest.pdb) and combined with the acetylated lysine molecule. I assigned the right atom types and so.
Then I saved peptide.off and peptide.mol2 files.
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 it correct for peptides to simulate them like that ? Or should I delete those atoms assigned and manually correct them before the simulation ?
If you can help me how to solve this problem and give me some hints if there is any easy way to simulate the acetylated lysine peptides, I would be very glad .
Best regards,
Berin Karaman
Medicinal Chemistry
Institute of Pharmacy
Martin-Luther-Universität Halle-Wittenberg
Wolfgang-Langenbeck-Str. 4
06120 Halle (Saale), Germany
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Received on Fri May 16 2014 - 01:30:03 PDT
