Dear Urszula,
> I run again the Ante_R.E.D. 1.4 and also Ante_R.E.D. 2.0 . R.E.D,
> but i am still getting errors when I am loading the mol2 file to the
> xleap ...
So by now, this is far better because by now (i) your charges are
correctly equivalenced in the pyridine group & (ii) I understand your
structure when I see the atom names ;-)
.<TRIPOS>ATOM
1 N 0.605380 0.819932 -0.576060 N 1 PYA -0.7057
2 H 0.174989 0.824523 -1.472280 H 1 PYA 0.3686
3 CA 0.730348 -0.452452 0.117596 CT 1 PYA 0.1959
4 HA 0.639473 -0.241084 1.173722 H1 1 PYA 0.0965
5 CB -0.369688 -1.423667 -0.320567 CT 1 PYA -0.0206
6 HB2 -0.233967 -1.663736 -1.367613 HC 1 PYA 0.0018
7 HB3 -0.227914 -2.352854 0.219720 HC 1 PYA 0.0018
8 CG -1.766459 -0.896904 -0.076042 CA 1 PYA 0.1963
9 CD1 -2.623650 -0.605483 -1.126238 CA 1 PYA -0.3512
10 HD1 -2.321269 -0.760458 -2.146784 HA 1 PYA 0.1613
11 CD2 -2.253978 -0.688025 1.209409 CA 1 PYA -0.3512
12 HD2 -1.651676 -0.902180 2.074037 HA 1 PYA 0.1613
13 CE1 -3.893742 -0.122764 -0.850677 CM 1 PYA 0.2935
14 HE1 -4.569416 0.106050 -1.656600 H4 1 PYA 0.0700
15 CE2 -3.537068 -0.201541 1.372658 CM 1 PYA 0.2935
16 HE2 -3.928313 -0.034089 2.360846 H4 1 PYA 0.0700
17 NZ -4.350531 0.082106 0.368715 NC 1 PYA -0.5622
18 C 2.117472 -1.058764 -0.143516 C 1 PYA 0.1611
19 O 2.279254 -1.956249 -0.927864 O 1 PYA -0.1216
Here, are the errors I get in LEaP (CB vs CM):
Could not find bond parameter for: CM - NC
Could not find bond parameter for: CM - NC
--> Use CA-NC by analogy in your own frcmod file
Building angle parameters.
Could not find angle parameter: CA - CA - CM
Could not find angle parameter: CA - CA - CM
--> Use CM-CM-C by analogy for instance
Could not find angle parameter: CA - CM - NC
--> Use CB-CA-NC by analogy for instance
Could not find angle parameter: HA - CA - CM
--> Use HA-CA-CA by analogy for instance
Could not find angle parameter: CA - CM - NC
Could not find angle parameter: HA - CA - CM
Could not find angle parameter: CM - NC - CM
--> Use CB-NC-CA by analogy for instance
Could not find angle parameter: H4 - CM - NC
Could not find angle parameter: H4 - CM - NC
--> Use HA-CM-N* by analogy for instance
Building proper torsion parameters.
** No torsion terms for CA-CM-NC-CM
** No torsion terms for CA-CM-NC-CM
** No torsion terms for CM-NC-CM-H4
** No torsion terms for H4-CM-NC-CM
---> Use X -CA-NC-X by analogy
(the number of path is 2)
regards, Francois
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Dec 07 2011 - 06:30:02 PST
