tleap adds hydrogen atoms from the template libraries if they don't exist.
If the hydrogen atoms cause naming conflicts for me, I typically remove them
before I load the structures in leap (with reduce -Trim).
Hope this helps,
Jason
2010/9/27 geyan <geyan.big.ac.cn>
> But in fact, the Modeller won't produce the Hydrogen atoms,while the
> confliciting atoms are the H atom after I reproduce the Modeller created
> structure in Amber.
>
>
> 2010-09-27
>
>
>
> geyan
>
>
>
> 发件人： Bill Ross
> 发送时间： 2010-09-27 18:16:03
> 收件人： amber
> 抄送：
> 主题： Re: [AMBER] can't save the PDB file to produce topology andcoordinates
> file
>
> > 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,
> One thing about leap is that it expects unique atom names in each
> residue, so if Modeller creates duplicate names, that would explain
> your symptom.
> Bill
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Sep 27 2010 - 04:30:05 PDT
