[AMBER] atom types for pyridine ...

From: Urszula Uciechowska <urszula.uciechowska.chem.umu.se>
Date: Mon, 5 Dec 2011 12:28:09 +0100

Dear amber users,

I have problems with proposing the atom types for the pyridine molecule ...

 1 N 0.605380 0.819932 -0.576060 N 1 PYA -0.4348 ****
  2 H 0.174989 0.824523 -1.472280 H 1 PYA 0.2971 ****
  3 CA 0.730348 -0.452452 0.117596 CT 1 PYA 0.0305 ****
  4 HA 0.639473 -0.241084 1.173722 H1 1 PYA 0.0603 ****
  5 CB -0.369688 -1.423667 -0.320567 CT 1 PYA -0.0171 ****
  6 HB2 -0.233967 -1.663736 -1.367613 HC 1 PYA 0.0573 ****
  7 HB3 -0.227914 -2.352854 0.219720 HC 1 PYA 0.0573 ****
  8 C8 -1.766459 -0.896904 -0.076042 CA 1 PYA 0.1171 ****
  9 C9 -2.623650 -0.605483 -1.126238 CA 1 PYA -0.3646 ****
 10 H9 -2.321269 -0.760458 -2.146784 HA 1 PYA 0.1558 ****
 11 C10 -2.253978 -0.688025 1.209409 CA 1 PYA -0.2597 ****
 12 H10 -1.651676 -0.902180 2.074037 HA 1 PYA 0.1277 ****
 13 C11 -3.893742 -0.122764 -0.850677 CA 1 PYA 0.3138 ****
 14 H12 -4.569416 0.106050 -1.656600 HA 1 PYA 0.0636 ****
 15 C12 -3.537068 -0.201541 1.372658 CA 1 PYA 0.2798 ****
 16 H11 -3.928313 -0.034089 2.360846 HA 1 PYA 0.0689 ****
 17 N13 -4.350531 0.082106 0.368715 NA 1 PYA -0.5709 ****
 18 C 2.117472 -1.058764 -0.143516 C 1 PYA 0.5924 ****
 19 O 2.279254 -1.956249 -0.927864 O 1 PYA -0.5743 ****
 

I have also tried to use CM atom type but still got errors...

> check x
Checking 'x'....
Checking parameters for unit 'x'.
Checking for bond parameters.
Checking for angle parameters.
Could not find angle parameter: CA - CA - NA
Could not find angle parameter: CA - CA - NA
Could not find angle parameter: CA - NA - CA
Could not find angle parameter: HA - CA - NA
Could not find angle parameter: HA - CA - NA
There are missing parameters.
Unit is OK.

/Urszula

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Received on Mon Dec 05 2011 - 04:00:02 PST
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