Dear all
Greetings !
I am a new user of Glycam .
I would like to build GAG molecule , for example
the Alpha - iduronic acid 2 - O sulfate ( a single residue )
for that I called the xleap of amber ,
1) I sourced the ff99 force field.
2)I sourced the GLYCAM_06h-12SB
3)i loaded the Sulfate.prep
then i did as given in the sulphating residue in Glycam
m = sequence { ROH 0uA}
set m.2.O2 charge -0.463
set m tail m.2.O2
m = sequence { m SUL}
charge m
>Total unperturbed charge: -2.000000
>Total perturbed charge: -2.000000
I fixed the charge on the O2 atom as said , since the total charge should
be an integer.
when I tried to write the prm and top files
it is giving the following error
Checking Unit.
WARNING: The unperturbed charge of the unit: -2.000000 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:
total 1 improper torsion applied
0 improper torsions in old prep form
Building H-Bond parameters.
Parameter file was not saved
>>>>>>>>>>>>>>>>>>>>>>>>>
can any one let me know what is wrong and is the sulfation done here is
correct ?
Thank you
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Received on Thu Aug 22 2013 - 12:00:04 PDT
