Hello,
On May 7, 2011, at 6:39 AM, Naveen Samala wrote:
> Hi,
>
>
>
> Would anyone please help me understand the following things from MTK++
> document- Side Chain Model example?
>
>
>
> 1. What do the below highlighted numbers mean in
> the file 1AMP_OH_sidechain.bcl? There is no number given to the hydroxyl
> residue OH1. Is there any reason in doing so?
>
>
>
> # Create HD1-1
>
> createResidue HD1 in CLR
>
> addToResidue /NAME/CLR/HD1 /NAME/1/HID-97 not bb
>
> # Create AS2-2 from ASP-179
>
> createResidue AS2 in CLR
>
> addToResidue /NAME/CLR/AS2 /NAME/1/ASP-179 not bb
>
> # Create AS1-3 from ASP-117
>
> createResidue AS1 in CLR
>
> addToResidue /NAME/CLR/AS1 /NAME/1/ASP-117 not bb
>
> # Create GL1-4 from GLU-152
>
> createResidue GL1 in CLR
>
> addToResidue /NAME/CLR/GL1 /NAME/1/GLU-152 not bb
>
> # Create HD2-5 from HID-256
>
> createResidue HD2 in CLR
>
> addToResidue /NAME/CLR/HD2 /NAME/1/HID-256 not bb
>
> # Create ZN1-6 from ZN-501
>
> createResidue ZN1 in CLR
>
> addToResidue /NAME/CLR/ZN1 /NAME/2/.ZN-501/ZN..
>
> # Create ZN2-7 from ZN-502
>
> createResidue ZN2 in CLR
>
> addToResidue /NAME/CLR/ZN2 /NAME/3/.ZN-502/ZN..
>
> # Create OH1-8 from MOH-935
>
> createResidue OH1 in CLR
>
> addToResidue /NAME/CLR/OH1 /NAME//MOH-935
>
>
I guess the "highlighted number" you mentioned means the number after /NAME/. It means the subunit number the residue belongs to. In general, each non-amino-acid residue, such as water, metal or ion, should be considered as a single subunit. There should be a number assigned to the OH1 case, but for some reason it didn't show up here, possibly due to a typo.
It might be helpful for you to understand this example with the following description: in the original PDB file, there are enzyme, 2 zinc ions, and several water molecules including the hydroxyl group. The enzyme has only 1 subunit, therefore, all amino acids belong to the 1st subunit. The zinc ions are the following units, therefore should be considered 2nd or 3rd subunit (notice the zinc ions are not actually 501st or 502nd residue in the PDB, however, they were originally numbered so). Then there might be n waters before MON-935, therefore the MON-935 should be subunit #(3+n+1).
>
> 2. In the following lines of code the methyl tereminating groups are
> bonded with certain angle and torsion to the residues atoms.
>
> # Methyl terminating groups (Add these after all other residue have been
> added)
>
> addFragment terminal/CH3 bd /NAME/CLR/HD1-1/.CB. ag /NAME/CLR/HD1-1/.CG. tr
> /NAME/CLR/HD1-1/.ND1 87.0
>
> addFragment terminal/CH3 bd /NAME/CLR/AS2-2/.CB. ag /NAME/CLR/AS2-2/.CG. tr
> /NAME/CLR/AS2-2/.OD2 170.0
>
> addFragment terminal/CH3 bd /NAME/CLR/AS1-3/.CB. ag /NAME/CLR/AS1-3/.CG. tr
> /NAME/CLR/AS1-3/.OD2 200.0
>
> addFragment terminal/CH3 bd /NAME/CLR/GL1-4/.CB. ag /NAME/CLR/GL1-4/.CG. tr
> /NAME/CLR/GL1-4/.CD. 288.0
>
> addFragment terminal/CH3 bd /NAME/CLR/HD2-5/.CB. ag /NAME/CLR/HD2-5/.CG. tr
> /NAME/CLR/HD2-5/.ND1 185.0
>
>
>
> I have a Cysteine residue bonded to FE metal via SG atom. How do I assigne
> the torsion in this case? Can I use Fe atom? For example:
>
> addFragment terminal/CH3 bd /NAME/CLR/CY1-1/.CB. ag /NAME/CLR/HD1-1/.SG. tr
> /NAME/CLR/FE1-1/.FE 87.0
>
>
The only function of these torsions is to keep the sidechains from sitting together or even overlapping each other. In you case, it depends on what geometry/coordination your cluster adopts. You can definitely use Fe atom and try some other torsion values.
>
> 3. In the below code, there is '..' after ZN atom and also '.O..'. What does
> it mean?
>
>
>
> createBond /NAME/CLR/ZN2/ZN.. /NAME/CLR/OH1/.O..
>
>
>
> I have a Fe4S4 cluster. Each Fe atom is bound to SG atom of cysteine residue
> and 3 S atoms of the cluster. Shell I assign bonds using createBond for
> each Fe with SG and three S of the cluster or only with SG atom of the
> cysteine residue?
>
> Do I need to assign bonds via createBond for each S atom in the cluster?
>
>
That "." actually means space. In AMBER, each atom has an atom type, usually in 1 or 2 letters, sometimes in 3 or 4 but never exceeds 4. That's why Martin leaves 4 letter space for each atom. For those unoccupied space, we use "." to fill up thus the code won't confuse. The atom types shown up in createBond section should be the same as that shown up in the previous createResidue section.
And yes, you need to assign bonds for each of them that bound to each Fe.
>
> Thanks,
>
> Naveen Samala
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Hope this helps.
Yue
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Received on Fri May 06 2011 - 19:00:02 PDT
