Try .SG. instead of .SG. The former is of size 4 while the latter (which caused
the error) is of size 3.
Yue
On Apr 23, 2012, at 8:21 AM, Fabrício Bracht wrote:
> 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 - 17:00:03 PDT
