Now I found the problem is caused by the confliciting H atom belong to the N(or CA?I'm not sure) of the initiate Met residue, which will produce two ATOM with same name:2H. But even if I delete one, the problem remains. Now what I choose to solve it is to remove all the Hydrogen atoms. In this way, I can save the parameter file. But I'm not sure whether it's a efficient method or I'm evading the problem.
2010-09-27
geyan
发件人： dhacademic
发送时间： 2010-09-27 08:52:25
收件人： AMBER Mailing List
抄送：
主题： Re: [AMBER] can't save the PDB file to produce topology andcoordinates file
There maybe something wrong with your structure generated from Modeller.
Please carefully check the atom name one by one to make sure that they are
compatible with amber nomenclature. Another choice is to delete all the
sidechains, keep backbone atoms only, and then load with tleap. This may be
a easier way to check the problem.
Hope this helps.
On Sun, Sep 26, 2010 at 12:43 AM, geyan <geyan.big.ac.cn> wrote:
> Hi,Amber friends,
> I met a strange problem. I use Modeller to produce a target protein
> structure. When I load it in Amber using loadpdb command and try to save it
> for furthure use, error message appears, first telling me that there are
> duplicating atoms, and then consequently informing saving parameter file
> failed. After I use ambpdb command to reproduce the structure, I found the
> duplicate ones.
> Now the point is even if I delete the same item manually to only leave
> one to produce parameter file, the error remains the same. I'm really
> helpless to figure this out.
> Hope your help!
>
> 2010-09-26
>
>
>
> geyan
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Sep 27 2010 - 03:30:05 PDT
