Dear Amber users,
for the last week or so, I have been trying to parametrize the copper center in a laccase. For this, I have been trying to use MCPB, with files based on the tutorial in the MTK++ handbook. Now, I can confirm that the tutorial "as is" works in my amber installation (so there doesn't seem to be anything wrong with it).
On the other hand, when I prepare my files, I've encountered several problems:
1st, I always get the following errors during the addHs or sidechains step:
### ### ### ###
### MTK++ Error ###
### Function: connections::assignStdAngles ###
### Message: Please assign angles before assigning MM parameters for molecule: CU
### ### ### ###
### ### ### ###
### MTK++ Error ###
### Function: connections::assignStdTorsions ###
### Message: Please assign torsions before assigning MM parameters for molecule: CU
### ### ### ###
Still, the system goes on, and I actually get some results (a protonated and/or sidechain file, depending on the operation I am performing).
When I look at the output pdb files, I see several strange results:
All coppers are grouped into one molecule. On the 1AMP tutorial, each Zn had their own chain, so I don't know what is happening there.
Also, if I have to define coppers as ATOM, if I define them at HETATM, the protonation step fails with:
1 Error in watProtonate ... exiting
terminate called after throwing an instance of 'MTKpp::MTKException'
Aborted (core dumped)
Also, I introduced two MOHs, which are part of the cluster. These are also considered to be a single molecule in the output files. Furthermore, after parametryzation, they are not protonated at all, resulting in two O2-, and not two OH-, as they should be.
Any suggestions as to what is going on? I'm just going crazy, because cannot find where I made the mistake...
Thank you very much,
Manuel
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Received on Wed Jun 26 2013 - 19:00:03 PDT
