Hello,
It is difficult to tell what is wrong without the pdb, could you please provide the one you're using? Did you try to load the pdb used in the tutorial into leap, does it work flawlessly?
Best regards,
Jean-Marc
Sent from my iPhone
> On 09 Jan 2016, at 23:40, Bin Wang <ben.wangbj.gmail.com> wrote:
>
> Dear Amber users,
>
> I followed the method in this website to install the AmberTools 15, and try
> to use the lipdi14 force field with Amber 11
> http://jswails.wikidot.com/installing-ambertools-14-and-older-amber
>
> Then I followed the Amber online tutorial 16 to get the membrane-protein
> structure.
> http://ambermd.org/tutorials/advanced/tutorial16/
>
> However, when I used xleap to load the pdb file of this membrane-protein
> structure, the xleap showed a lot of errors such as these:
>
> Created a new atom named: C11 within residue: .R<PS 1969>
> Created a new atom named: O12 within residue: .R<PS 1969>
> One sided connection. Residue: default_name missing connect1 atom.
> Creating new UNIT for residue: PS sequence: 1972
> One sided connection. Residue: missing connect0 atom.
> Created a new atom named: N31 within residue: .R<PS 1972>
> Created a new atom named: HN1A within residue: .R<PS 1972>
> Created a new atom named: HN1B within residue: .R<PS 1972>
> Created a new atom named: HN1C within residue: .R<PS 1972>
> Created a new atom named: C32 within residue: .R<PS 1972>
> Created a new atom named: H2A within residue: .R<PS 1972>
> Created a new atom named: C33 within residue: .R<PS 1972>
> Created a new atom named: O35 within residue: .R<PS 1972>
> Created a new atom named: O36 within residue: .R<PS 1972>
>
>
> It seems that the xleap doesn't recognize the PS and PA lipid units in the
> pdb file. I think I followed every step according to these tutorials, but
> couldn't find out why it didn't work.
>
> Could anybody give me some suggestions? Thank you very much!
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Received on Sun Jan 10 2016 - 22:00:03 PST
