I'm not sure if this is the cause of your errors, but there may be a
problem with the residue names that you are using to create your model
(e.g. AC1 or NE1 and others). All the residue names should be defined in
the libraries that you load in (i.e. NAME_params.xml, NAME.xml, and all
standard libraries).
I think that when you use "createResidue AC1 in CLR" for example, the
residue AC1 is unrecognized and therefore producing an error. You should
either use "ACE" (and "NME" instead of NE1) or use the following command
to copy the standard residues to AC1 or NE1.
copyStdResidue aminoAcids94/ACE NAME/AC1
copyStdResidue aminoAcids94/NME NAME/NE1
Let me know if this helps,
Hashem
On 5/3/11 12:31 PM, "Manish" <manish.datt.hotmail.com> wrote:
>Hi All,
>
>
>
>I'm trying to MCPB to calculate parameters for tetrahedrally coordinated
>Zinc ion in a protein following the MTK++ manual. The first part with the
>sidechain runs fine. But with the large part the calculations are getting
>stuck. These have been running for 60 hours. Is it expected? Tail of the
>log
>file is below:
>
>### ### ### ###
>
>### MTK++ Info ###
>
>### Function: watProtonate::setup ###
>
>### Message:
>
>Number of sphere grid points = 1098
>
>Allocating sphereGridCoords: 3294 ints
>
>Allocating maxPairs: 1098 ints
>
>Allocating Hs: 106506 ints
>
>Allocating lonePairs: 213012 ints
>
>### ### ### ###
>
>
>
>### ### ### ###
>
>### MTK++ Info ###
>
>### Function: protonate::runMol ###
>
>### Message: CLR
>
>### ### ### ###
>
>--------------------------------------------------------------------------
>--
>----
>
>
>
>Attached is the complete log file. Please suggest if should try something
>else or just run longer.
>
>
>
>Thanks,
>
>
>
>Manish
>
>
>
>
>
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Received on Tue May 03 2011 - 12:30:03 PDT
