Dear amber users,
I have problem with the atom types in my mol2 file,
Could not find angle parameter: HC - CT - S
Could not find angle parameter: HC - CT - S
Could not find angle parameter: HC - CT - N
Could not find angle parameter: S - CT - N
There are missing parameters.
my mol2 file contains...
1 CA -0.995684 -0.049134 0.008736 CT 1 TLS -0.0334 ****
2 HA -0.799138 -0.052416 -1.053068 H1 1 TLS 0.0576 ****
3 CB -0.099712 -1.111991 0.679776 CT 1 TLS -0.1862 ****
4 HB2 -0.430116 -2.098640 0.367872 HC 1 TLS 0.0919 ****
5 HB3 -0.234107 -1.046445 1.752460 HC 1 TLS 0.0919 ****
6 CG 1.349337 -0.960779 0.324248 CT 1 TLS 0.2593 ****
7 C -2.453054 -0.425514 0.278900 C 1 TLS 0.6347 ****
8 O -2.963900 -0.170866 1.336578 O 1 TLS -0.5514 ****
9 CD 2.346703 -0.594866 1.145530 CT 1 TLS -0.2568 ****
10 HD2 2.286202 -0.338841 2.182414 HC 1 TLS 0.2218 ****
11 CE 2.992125 -1.060567 -1.124597 CT 1 TLS 0.1351 ****
12 HE2 3.502748 -1.213812 -2.055533 HC 1 TLS 0.1631 ****
13 SD 3.846789 -0.572802 0.290248 S 1 TLS -0.0190 ****
14 N -0.753783 1.268637 0.538283 N 1 TLS -0.4051 ****
15 H -1.138646 1.446976 1.442404 H 1 TLS 0.2857 ****
16 ND1 1.735334 -1.221817 -0.979128 N 1 TLS -0.4894 ****
.<TRIPOS>BOND
1 1 2 1
2 1 3 1
3 1 7 1
4 1 14 1
5 3 4 1
6 3 5 1
7 3 6 1
8 6 9 1
9 6 16 1
10 7 8 1
11 9 10 1
12 9 13 1
13 11 12 1
14 11 13 1
15 11 16 1
16 14 15 1
.<TRIPOS>SUBSTRUCTURE
1 TLS 1 **** 0 **** ****
what is the right atom type for the S and N
best regards
Urszula
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Nov 28 2011 - 23:30:03 PST
