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 Sat Jan 09 2016 - 15:00:03 PST
