I also tried to replace CU to ZN in my protein.The error dispeared,does it mean I need to add more parameters for CU?what I need to do?
------------------ 原始邮件 ------------------
发件人: "wenjuanli93";<wenjuanli93.gmail.com>;
发送时间: 2014年12月24日(星期三) 中午12:42
收件人: "amber"<amber.ambermd.org>;
主题: [AMBER] Errors during Adding hydrogen atoms to the PDB file（MCPB program）
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Dec 23 2014 - 21:30:02 PST
