Thank you sir for your kind response . This is my main pdb (2rd6-new.pdb) and after capping pdb (2rd6-leap-1.pdb).I have attached these pdbsin this mail.Thanks and regards,saikat
On Thursday, 15 June 2017 2:04 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
Do you have a TER between chains in the pdb?
Bill
<div>-------- Original message --------</div><div>From: Saikat Pal <saikatpaliitg.yahoo.com> </div><div>Date:06/15/2017 12:29 AM (GMT-08:00) </div><div>To: AMBER Mailing List <amber.ambermd.org> </div><div>Subject: [AMBER] problem regarding ACE capping of the protein terminal of
the PDB </div><div>
</div>Dear Amber users,
For ACE and NME capping of the protein terminal, I have followed these steps :
1) Get the PDB
2)Add hydrogens
3)Load into xleap
4)xleap will add OXT terms to ends of chains
5) In adding NME, just remove the OXT oxygen and in that place, put the N atom of NME (if adding a new atom, atom number is zero. Keep the residue
number as it is)
6) To add ACE groups, from each N terminal, remove two hydrogens bound to N eg:- H1,H2 or H3 Then put the ACE carbon atom
7) Now load the file into xleap
There will be some messages about splitting residues because ACE and the following amino acids as well as NME and the following amino acids both have the same residue numbers
8)Some unknown hydrogens will be added into the residue after the ACE.
1>In case of NME it works fine, but in case of ACE two residue are merged to each other (ACE and 1st residue of the protein in my pdb it is LYS).
What should I do ?? plz help me out.2>how can I remove H from protein in PDB ??
Thanks and regards,
Saikat
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Received on Thu Jun 15 2017 - 04:00:03 PDT
