[AMBER] Error in conversion from charmmgui to AMBER format

From: Souvik Dey <sdey8.uic.edu>
Date: Thu, 24 Jan 2019 18:21:03 -0600

Hi All,

I am trying to convert a protein lipid system that was generated from
CHARMM-GUI into Amber format. So, initially I used charmmlipid2amber.py
script which runs fine.

Then, I remove the hydrogen atoms from the pdb using pdb4amber. It shows no

I also modify the name of Histidine and change a naming convention for ILE.

However, when I try to run tleap using lipid17 and Amber14SB force field, I
get the following error:

*Error: Comparing atoms*
* .R<OL 3>.A<C13 11>, *
* .R<OL 3>.A<H2R 9>, *
* .R<OL 3>.A<H2S 10>, and *
* .R<PE 2>.A<C21 32> *
* to atoms*
* .R<OL 3>.A<C13 11>, *
* .R<PA 1>.A<C12 44>, *
* .R<OL 3>.A<H2S 10>, and *
* .R<PE 2>.A<C21 32> *
* 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 !*

Could someone please guide me as to where i am going wrong? Do I need to
modify something in the charmmlipid2amber.py file?

Thanks in advance.

Souvik Dey
Graduate Student
Department of Chemistry
University of Illinois Chicago
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Received on Thu Jan 24 2019 - 16:30:03 PST
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