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
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
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?
Thanks,
Naveen Samala
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Received on Fri May 06 2011 - 16:00:02 PDT
