From: Benjamin D Madej <>
Date: Mon, 9 Jun 2014 19:02:09 +0000

Hi James,

Sorry about the problem with It was a problem with residue numbering. I am currently working on getting the fix out to all users.

Here is an updated version of the script for you to use now:

As for your protein system, it appears that that LEaP may be trying to connect a lipid molecule and a protein molecule. Make sure that you have appropriate TER cards in your structure. For example, the protein chains must be ended with a TER card and the lipids should follow the Lipid14 PDB format.

All the best,
Ben Madej
UCSD Chemistry and Biochemistry

From: James Starlight []
Sent: Friday, June 06, 2014 9:26 AM
To: AMBER Mailing List
Subject: Re: [AMBER]

also below error have been appeared during processing of the rhodopsin by
tleap wih he same membrane (this time I had no problem with the conversion
of charm to amber pdb in comparison to the above case) using rhodopsin from
the tutorial.


source leaprc.ff12SB
source leaprc.lipid14
m = loadpdb rho_amber.pdb
#check m
saveamberparm m rhodopsin.prmtop rhodopsin.inpcrd


        .R<PA 349>.A<C13 41>,
        .R<ALA 348>.A<C 9>,
        .R<PA 349>.A<H2R 45>, and
        .R<PA 349>.A<H2S 46>
       to atoms
        .R<PA 349>.A<C13 41>,
        .R<PC 1>.A<C11 5>,
        .R<PA 349>.A<H2R 45>, and
        .R<ALA 348>.A<C 9>
       This error may be due to faulty Connection atoms.
!FATAL ERROR----------------------------------------
!FATAL: In file [chirality.c], line 142
!FATAL: Message: Atom named C11 from PC did not match !

2014-06-06 16:40 GMT+02:00 James Starlight <>:

> Dear Amber's users!
> I have a problem in the conversion charm gui PDB to amber PDB
> -i b2ar_charm.pdb -c
> $AMBERHOME/AmberTools/src/etc/charmmlipid2amber/charmmlipid2amber.csv -o
> b2ar_amber.pdb
> Error: Number of atoms in residue does not match number of atoms in
> residue in replacement data file
> here you can find my pdb
> I suppose this is some bud isn't it?
> James
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Received on Mon Jun 09 2014 - 12:30:02 PDT
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