[AMBER] 回复: Errors during Adding hydrogen atoms to the PDB file(MCPB program)

From: wjli <wenjuanli93.gmail.com>
Date: Wed, 24 Dec 2014 13:01:27 +0800

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
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Received on Tue Dec 23 2014 - 21:30:02 PST
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