Hi Wenjuan,
The addHs function in MCPB always met problems. You can use another software to add the hydrogens first and then use the pdb file which already has hydrogens on it in the further modeling.
Best,
Pengfei
On Dec 24, 2014, at 12:01 AM, wjli <wenjuanli93.gmail.com> wrote:
> 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 Thu Jan 08 2015 - 09:00:04 PST
