Dear Urszula,
CT - CT - O does not exist; it should be CT - CT - OS or CT - CT - OH
or ... ; but for sure not CT - CT - O
OH - CT - O same remark...
H1 - CT - N3 should be replaced by HP - CT - N3 or by H1 - CT - NT...
see $AMBERHOME/dat/leap/parm/parm99.dat for the definition of the
atom types...
or see Cornell, et al. J. Am. Chem. Soc. , 117, 5179-5197 (1995)
Table 1. List of Atom Types
regards, Francois
> I am trying to find proper atom types for my small molecule. However
> I am getting some errors whenever I put any changes.
>
> Thank you in advance for your suggestions.
>
> from xleap:
>
> Checking 'x'....
> Checking parameters for unit 'x'.
> Checking for bond parameters.
> Could not find bond parameter for: CT - O
> Checking for angle parameters.
> Could not find angle parameter: CT - CT - O
> Could not find angle parameter: OH - CT - O
> Could not find angle parameter: H1 - CT - N3
> Could not find angle parameter: H1 - CT - N3
> There are missing parameters.
> Unit is OK.
>
>
> molecule:
>
> .<TRIPOS>MOLECULE
> BAL
> 13 12 1 0 0
> SMALL
> No Charge or Current Charge
>
>
> .<TRIPOS>ATOM
> 1 C1 0.1700 -1.0030 0.0170 CT 1 BAL -0.49379
> 2 C4 -0.8840 0.0770 0.0630 CT 1 BAL 0.81232
> 3 O5 -2.1030 -0.3960 -0.2950 OH 1 BAL -0.68842
> 4 H9 -2.7230 0.3470 -0.2490 HO 1 BAL 0.48217
> 5 O6 -0.7090 1.2300 0.3760 O 1 BAL -0.61604
> 6 H12 0.1920 -1.4040 -1.0010 HC 1 BAL 0.23828
> 7 H13 -0.1640 -1.8180 0.6680 HC 1 BAL 0.23056
> 8 C2 1.5590 -0.5110 0.4220 CT 1 BAL -0.18107
> 9 H10 1.5140 -0.1180 1.4480 H1 1 BAL 0.16815
> 10 H11 2.2290 -1.3750 0.4350 H1 1 BAL 0.18663
> 11 N3 2.0770 0.4520 -0.5530 N3 1 BAL -0.85573
> 12 H7 3.0650 0.6240 -0.4010 H 1 BAL 0.35170
> 13 H8 1.5930 1.3390 -0.4540 H 1 BAL 0.36524
> .<TRIPOS>BOND
> 1 1 2 1
> 2 1 6 1
> 3 1 7 1
> 4 1 8 1
> 5 2 3 1
> 6 2 5 2
> 7 3 4 1
> 8 8 9 1
> 9 8 10 1
> 10 8 11 1
> 11 11 12 1
> 12 11 13 1
> .<TRIPOS>SUBSTRUCTURE
> 1 BAL 1 TEMP 0 **** **** 0 ROOT
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Received on Fri Apr 12 2013 - 07:00:12 PDT
