[AMBER] not able to build prmtop and inpcrd with glycam

From: lara lara <lara.4884.gmail.com>
Date: Thu, 22 Aug 2013 14:58:09 -0400

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
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