Thread: Re: [apbs-users] O2' atom to DNA (PDB2PQR)
Biomolecular electrostatics software
Brought to you by:
sobolevnrm
From: Baker, N. <Nat...@pn...> - 2012-09-13 02:15:40
|
Hi Abusaud – I passed this problem along to Kyle Monson for investigation. Thanks, __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: +1-509-375-3997 http://nabaker.me<http://nabaker.me/> From: Abusaud [mailto:abu...@gm...] Sent: Tuesday, September 11, 2012 11:40 AM To: apb...@go... Subject: [apbs-users] O2' atom to DNA (PDB2PQR) I tried to convert ssAAA.pdb to pqr. I found there is an O2 atom added. Could you pleases tell me if this process right or no. I am attaching the pdb and pqr files. ---------------stdout.txt--------------- Checking for missing heavy atoms... Missing O2' in ADE D 1 Missing O2' in ADE D 2 Missing O2' in ADE D 3 Missing 3 out of 63 heavy atoms (4.76 percent) - Will attempt to repair. Rebuilding missing heavy atoms... Added O2' to ADE D 1 at coordinates -4.519 4.960 -2.165 Added O2' to ADE D 2 at coordinates -6.415 1.521 1.299 Added O2' to ADE D 3 at coordinates -5.868 -2.290 4.844 Done. |