The atom type for O2 can no longer be Oh (because it is no longer a
hydroxyl oxygen).
On Tue, Sep 10, 2013 at 3:29 PM, lara lara <lara.4884.gmail.com> wrote:
> Dear AMber !
>
> I have an leap error when i generated the glycam residues
>
> I would like to join two sugar units with 1O of first to the second that is
> done by the letter code
> but I am not able to add sulfate on the 1O free sugars.
>
> like I want to add sulfate in position 2 of first residue.
>
> I used the command as below , How to fix this .
>
>> m = sequence { 1uA}
>> edit m
>> set m tail m.1.O1
>> m = sequence { m 2uA}
>> edit m
>> remove m m.1.H2O
>> set m.1.O2 charge -0.4630
>> set m tail m.1.O2
>> m = sequence { m SUL}
>> edit m
>> set m.2.O2 charge -0.4630
>> set m tail m.2.O2
>> m = sequence { m SUL}
>> edit m
>> saveamberparm m l.prmtop l.inpcrd
> Checking Unit.
> WARNING: The unperturbed charge of the unit: -4.000000 is not zero.
>
> -- ignoring the warning.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Could not find bond parameter for: Oh - S
> Building angle parameters.
> Could not find angle parameter: Cg - Oh - S
> Could not find angle parameter: Oh - S - O2
> Could not find angle parameter: Oh - S - O2
> Could not find angle parameter: Oh - S - O2
> Building proper torsion parameters.
> ** No torsion terms for Cg-Cg-Oh-S
> ** No torsion terms for Cg-Cg-Oh-S
> ** No torsion terms for Cg-Oh-S-O2
> ** No torsion terms for Cg-Oh-S-O2
> ** No torsion terms for Cg-Oh-S-O2
> ** No torsion terms for H1-Cg-Oh-S
> Building improper torsion parameters.
> old PREP-specified impropers:
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Tue Sep 10 2013 - 13:00:03 PDT
