Hi there. I am trying to create parameters in order to simulate an
enzime with 2CYS residues and a histidine residue bound to Zn atom in
the active site. I am using amber12 and MCPB to do this. I am
basically using the same scripts given by the MTK++ manual (MCPB
section) and trying to adapt them to my reality. When performing the
NAME_sidechain.bcl part, I've noticed that there is this section with
"copyStdResidue", "copyAtomType", and "setAtomType" that I assume are
getting the atom names and residue names from the forcefield database
and simply redirecting them to the MCPB routine, right? In the
original file, there is a section saying "# Create new atom types",
but these new atom types are not used anywhere else in the script.
Regarding my system, I have not found the correct way to deal with the
SG atom in CYM residue. I've read in another post that the correct
atom name for parm94 is actually SH (and not SG). So I've created a
section in the script that goes like this:
copyAtomType parm94/SH NAME/SH
setAtomType NAME/CY2/.SG NAME/SH
This is for one of my cysteine residues, named later on CY2 by the lines:
# Create CY2-2 from CYM-89
createResidue CY2 in CLR
addToResidue /NAME/CLR/CY2 /NAME/1/CYM-89 not bb
When i run MCPB with this script I get an error in the log saying
### ### ### ###
### MTK++ Error ###
### Function: MCPB::setAtomType ###
### Message: Error in setAtomType -> atom name must be of size 4 ... exiting
### ### ### ###
I'm kinda lost here. Wonder if you could give me a help.
Thanks
Fabrício
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Received on Mon Apr 23 2012 - 08:30:04 PDT
