Dear Gözde,
I also came across this error message a while ago.
The issue seems to be, that charmmlipid2amber.py checks the residue
sequence number in columns 22-26 (see code lines 83, 85, 94). However,
after solvation, the residue numbers often exceed 10000. The PDB file
which CHARMM-GUI gives you also has column 27 occupied with the last
digit of your five digit residue number.
For me the problem was fixed, when I naively changed the '[22:26]' in
these lines of code to '[22:27]'.
Best regards,
Michele
Am 25.04.2015 um 13:35 schrieb Gözde YALÇIN:
> Dear Amber's users
>
> I have faced with a problem when I convert charmm-gui membrane pdb to amber
> pdb. I tried all reasons that you said before about this problem. But the
> error didn't change.This is the error message:
>
> gozde.amber2:~/dop3/charmm-gui> charmmlipid2amber.py -i step5_assembly.pdb
> -o amber.pdb
> Error: Number of atoms in residue does not match number of atoms in residue
> in replacement data file
>
> Could you help me if you have an idea, please?
>
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Received on Sat Apr 25 2015 - 06:30:02 PDT
