AMBER Archive (2004)

Subject: Re: AMBER: Bad contacts

From: bybaker_at_itsa.ucsf.edu
Date: Wed Jun 09 2004 - 12:02:01 CDT

Dear Carlos and Bill:

Thank you for the suggestions on my questions about bad contacts.

I removed the bad coordinates manually from the .pdb file. Most of them
are related to HIS – HID. I loaded the modified structure again with
SwissPDB Viewer. This time, most of the bad contacts (HID residues) are
gone, except two, HID162 and LYS172, still remain. This structure is
subjected to energy minimization for 1000 steps in Sander (Amber7), but
no change is made in either energy level or structure geometry. These two
residues still make ‘aa clashing’ in SwizzPDB Viewer.

I look at the file, really hard to tell which parts are wrong. The way
used to fix bad coordinates works well for the HID residues, except
HID162. In the 3D-structure, there is a H-bond observed between HID162
and LYS172. Could anyone please give me some suggestions? The follow is
the copy of .pdb file of the two residues:

Best regard

Bo Yang

------Start-----

ATOM 2526 N HID 162 34.384 45.150 17.166 1.00 99.99
ATOM 2527 CA HID 162 35.289 46.259 16.934 1.00 99.99
ATOM 2528 C HID 162 35.829 46.350 15.498 1.00 99.99
ATOM 2529 O HID 162 36.691 45.550 15.159 1.00 99.99
ATOM 2530 CB HID 162 36.492 46.150 17.865 1.00 99.99
ATOM 2533 CG HID 162 36.164 46.050 19.317 1.00 99.99
ATOM 2534 ND1 HID 162 36.983 45.528 20.285 1.00 99.99
ATOM 2536 CE1 HID 162 36.348 45.647 21.455 1.00 99.99
ATOM 2538 NE2 HID 162 35.169 46.241 21.332 1.00 99.99
ATOM 2539 CD2 HID 162 35.025 46.458 19.962 1.00 99.99
ATOM 2543 H HID 162 34.775 44.223 17.170 1.00 99.99
ATOM 2544 HA HID 162 34.769 47.151 17.217 1.00 99.99
ATOM 2545 2HB HID 162 37.062 45.262 17.596 1.00 99.99
ATOM 2546 3HB HID 162 37.138 47.020 17.727 1.00 99.99
ATOM 2547 HD1 HID 162 37.905 45.147 20.152 1.00 99.99
ATOM 2548 HE1 HID 162 36.734 45.309 22.401 1.00 99.99
ATOM 2549 HD2 HID 162 34.170 46.821 19.445 1.00 99.99

ATOM 2672 N LYS 172 37.498 42.503 14.814 1.00 99.99
ATOM 2673 CA LYS 172 37.523 41.724 16.034 1.00 99.99
ATOM 2674 C LYS 172 36.169 41.550 16.711 1.00 99.99
ATOM 2675 O LYS 172 35.448 42.518 16.904 1.00 99.99
ATOM 2676 CB LYS 172 38.512 42.439 16.946 1.00 99.99
ATOM 2677 CG LYS 172 38.984 41.542 18.071 1.00 99.99
ATOM 2678 CD LYS 172 39.750 40.357 17.459 1.00 99.99
ATOM 2679 CE LYS 172 40.193 39.538 18.606 1.00 99.99
ATOM 2680 NZ LYS 172 40.850 38.236 18.363 1.00 99.99
ATOM 2681 H LYS 172 37.175 43.456 14.898 1.00 99.99
ATOM 2682 HA LYS 172 37.841 40.732 15.757 1.00 99.99
ATOM 2683 2HB LYS 172 39.373 42.749 16.354 1.00 99.99
ATOM 2684 3HB LYS 172 38.029 43.330 17.346 1.00 99.99
ATOM 2685 2HG LYS 172 39.648 42.106 18.722 1.00 99.99
ATOM 2686 3HG LYS 172 38.124 41.207 18.662 1.00 99.99
ATOM 2687 2HD LYS 172 39.080 39.736 16.893 1.00 99.99
ATOM 2688 3HD LYS 172 40.595 40.693 16.857 1.00 99.99
ATOM 2689 2HE LYS 172 40.853 40.152 19.213 1.00 99.99
ATOM 2690 3HE LYS 172 39.245 39.348 19.118 1.00 99.99
ATOM 2691 1HZ LYS 172 41.690 38.338 17.818 1.00 99.99
ATOM 2692 2HZ LYS 172 41.064 37.779 19.240 1.00 99.99
ATOM 2693 3HZ LYS 172 40.213 37.609 17.903 1.00 99.99

-----End-----

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