Hello,
i'm actually working on a lipid membrane and i'm familliar with this issues,
to solve it i recommand the following step :
-in chimera : save your files in amber mode (not hybrid36 which is the
standard in chimera )
Then use the program pdb4amber :
>$AMBERHOME/bin/pdb4amber -i input.pdb --reduce --add-missing-atoms -o
output.pdb -l file.log
and then remember to charge in tleap :
>source leaprc.lipid17
>source leaprc.protein.ff14SB
I hope it helps
> Deal all,
>
> I follow the tutorial to build the membrane-water system. And tleap can
> read the final structure. Then, I put a protein in the membrane-water
> system (the protien locates in the water not the membrane). And I use
> chimera to do it. But when I use the tleap to read the complex, it shows:
> Error: Comparing atoms
> .R<OL 3>.A<C13 11>,
> .R<OL 3>.A<H2R 9>,
> .R<OL 3>.A<H2S 10>, and
> .R<PC 2>.A<C21 41>
> to atoms
> .R<OL 3>.A<C13 11>,
> .R<PA 1>.A<C12 44>,
> .R<OL 3>.A<H2S 10>, and
> .R<PC 2>.A<C21 41>
> This error may be due to faulty Connection atoms.
> !FATAL ERROR----------------------------------------
> !FATAL: In file [chirality.c], line 142
> !FATAL: Message: Atom named C12 from PA did not match !
> !
> !ABORTING.
>
> I do not understand the information above. It seems that the chimera
> modified the membrane automatically, and the result is not compatible with
> tleap. Is there any method or any software can avoid this problem?
>
> Thanks!
>
>
>
> xmgign.126.com
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>
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Received on Mon Jun 03 2019 - 02:30:02 PDT
