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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Received on Tue Sep 10 2013 - 13:00:02 PDT
