AMBER Archive (2005)

Subject: Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list

From: David A. Case (case_at_scripps.edu)
Date: Mon Nov 14 2005 - 11:01:25 CST

On Fri, Nov 11, 2005, Nitin Bhardwaj wrote:

> Thanks fo replying again. The lipids are not close to each other. I
> created the second lipid by copying the first lipid and moved the
> second away along the x-axis by 8 Ang. So they are approx 8 Ang away.
> And the atoms that are being connected are ~9 Ang away. C67 is present
> in the structure. Its the second last carbon in the longer tail of the
> lipid.
>
>
> I am at my wit's end.

So am I, since I can't reproduce the behavior you are seeing. Just to be
clear, here is what I did:

source leaprc.ff94
loadAmberPrep popc.prepin
loadAmberParams popc.frcmod
x = loadPdb popc.pdb (the version with two lipids)
edit x (to confirm that there are no bonds bewteen the two lipids)
saveAmberParm x prmtop prmcrd

There is nothing funny around atom C67, no bonds between the two lipids, etc.
There were no errors or messages about superimposing torsions.

What compiler and OS are you using? Do you have access to any other sort
of machine that could be used to see if this is an architecture problem we
haven't run into before?

...regards...dac

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