Dear Amber members,
I have the same question with Manuel (I find in Amber Archive Jun 2013,
http://archive.ambermd.org/201306/0690.html).Sadly,it have no reply about following errors:
during the addHs 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
### ### ### ###
You can see my protein containing copper ions.So I try again to use CU（the third time using FE）to replace ZN，the same error occured.And I also find the waring:
### ### ### ###
### MTK++ Warning ###
### Function: pdbParser ###
### Message: Can't determine 1-letter code for CU. Using 'X'.
### ### ### ###
### ### ### ###
### MTK++ Warning ###
### Function: pdbParser ###
### Message: Can't determine 1-letter code for FE. Using 'X'.
I think it's strange because the file metals.xml and metalparm.xml include FE and CU.
I look forward to your reply!
wjli
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Received on Tue Dec 23 2014 - 21:00:02 PST
