Re: [AMBER] Some errors for the membrane system

From: Monsurat M. Lawal <>
Date: Wed, 1 Dec 2021 14:43:13 -0500


I have embedded my protein in POPE with CHARMM-GUI and followed this
tutorial ""
for the simulation.

However, this error (like this 2014 thread
and 2019 thread keeps popping

I have checked and noticed there are several connectivity issues within the
modeled membrane, that cannot be sorted manually. Our group has written
some python lines to sort the connections after converting to .xyz Tinker
file, which works. But this is not the same for .pdb file to AMBER files.
So far, all the suggestions (previous threads) did not work to fix this
error towards generating inpcrd and topology files for simulation.

I humbly ask for help.

ERROR: Comparing atoms

        .R<PA 1259>.A<C13 41>,

        .R<GLU 1258>.A<C 14>,

        .R<PA 1259>.A<H2R 45>, and

        .R<PA 1259>.A<H2S 46>

       to atoms

        .R<PA 1259>.A<C13 41>,

        .R<PE 1>.A<C11 5>,

        .R<PA 1259>.A<H2R 45>, and

        .R<GLU 1258>.A<C 14>

       This error may be due to faulty Connection atoms.

!FATAL ERROR----------------------------------------

!FATAL: In file [chirality.c], line 142

!FATAL: Message: Atom named C11 from PE did not match !



Best regards,
Monsurat M. Lawal
Postdoctoral associate
Department of Chemistry
Virginia Tech, Blacksburg
Virginia 24060, USA.
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Received on Wed Dec 01 2021 - 12:00:02 PST
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