Hi,
As David explained, we need to explicitly assign charge and bond on
the carbon connecting to sulfate group. For heparin (just a
disaccharide unit) my script are like:
source leaprc.GLYCAM_06j-1
lig=loadpdb 1_AMBER.pdb
set lig.2.O2 charge -0.481
set lig.3.O4 charge -0.413
set lig.3.O6 charge -0.450
bond lig.2.O2 lig.6.S1
bond lig.3.O4 lig.5.S1
bond lig.3.O6 lig.4.S1
bond lig.2.O4 lig.3.C1
saveamberparm lig dehydr.parm7 dehydr.rst7
quit
EOF
PS: If you remove "LINK" record from glycam-web output pdb file, you
might need to put more bond commands to join monosaccharide units.
..S
On Mon, Apr 24, 2017 at 11:56 PM, David Thieker <[log in to unmask]> wrote:
> Hi Neha,
>
> When working with modified residues in GLYCAM, charges of the attaching
> oxygen must be changed and bonds must be explicitly set. The complaints
> about missing parameters are a result of tleap incorrectly bonding the
> molecule. Here is a nice tutorial for how this works, with an example for
> sulfated residues.
>
> Since heparan sulfate commonly has N-sulfated glucosamine residues, our lab
> has created a set of prep files with NS built into the residue. This is
> unusual for GLYCAM files, but is true for those residue names ending in S
> (i.e. UYS). So, when you create the tleap input, you can skip the N-sulfate
> for those residues.
>
> I'm out of town this week, but can send an example tleap input when I return
> if you are still having problems.
>
> Best,
> David
>
> On Sun, Apr 23, 2017 at 11:22 PM, Neha Gandhi <[log in to unmask]>
> wrote:
>>
>> Hello,
>>
>> I tried to build heparin fragment using GAG builder.
>> The sequence is [UYS-YuA1]3-OME (see attached pdb file). I now want to use
>> this pdb file in AMBER16.
>>
>> I have loaded uronic acid and GlcNA prep files in tleap however, it
>> complains about missing parameters
>>
>> total atoms in file: 299
>> > check m1
>> Checking 'm1'....
>> WARNING: There is a bond of 4.102736 angstroms between:
>> ------- .R<YuA 3>.A<O2 18> and .R<UYS 4>.A<C1 1>
>> WARNING: There is a bond of 5.096146 angstroms between:
>> ------- .R<YuA 5>.A<O2 18> and .R<UYS 6>.A<C1 1>
>> WARNING: There is a bond of 4.119469 angstroms between:
>> ------- .R<YuA 7>.A<O2 18> and .R<UYS 8>.A<C1 1>
>> WARNING: There is a bond of 5.112499 angstroms between:
>> ------- .R<YuA 9>.A<O2 18> and .R<UYS 10>.A<C1 1>
>> WARNING: There is a bond of 4.305349 angstroms between:
>> ------- .R<YuA 11>.A<O2 18> and .R<UYS 12>.A<C1 1>
>> WARNING: There is a bond of 7.910717 angstroms between:
>> ------- .R<245 13>.A<O2 16> and .R<SO3 14>.A<S1 1>
>> ERROR: The unperturbed charge of the unit: -23.535000 is not integral.
>> WARNING: The unperturbed charge of the unit: -23.535000 is not zero.
>> Checking parameters for unit 'm1'.
>> Checking for bond parameters.
>> Could not find bond parameter for: Ck - C
>> Checking for angle parameters.
>> Could not find angle parameter: Os - S - Os
>> Could not find angle parameter: C - Ck - Ck
>> Could not find angle parameter: Ck - C - O2
>> Could not find angle parameter: Ck - C - O2
>> Could not find angle parameter: Os - Ck - C
>> There are missing parameters.
>> check: Errors: 1 Warnings: 7
>>
>
>
>
> --
> David F. Thieker
> PhD Candidate
> Biochemistry and Molecular Biology
> Complex Carbohydrate Research Center
> University of Georgia, Athens, GA
>
>
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