Dear Urszula,
Besides what told you Dr Case, I would use the NC atom type for
nitrogen in 6 member rings; and CB-CA-NC & CB-CB-NC are known...
regards, Francois
> 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 - 22:30:03 PST
