AMBER Archive (2005)

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

From: Nitin Bhardwaj (nbhardwaj_at_gmail.com)
Date: Tue Nov 15 2005 - 18:11:31 CST

Dear dac,
 Thanks for replying. I did exactly what you did above. But I was
still getting the same set of errors.
Then I started adding the lipids in sequence to the PDB file and
loaded them. First I loaded the file with 1 lipid. Then I added the
second lipid to the file and loaded it. it went fine. I then added 2
more lipids. So 2->4->8->16->32 lipids and finally 64 lipids. There
was no error then.
I have no explanation for this but it worked. Everything is fine..
atomtypes/bonds/charges. There are no unwated bonds. when I check my
unit, there are some warnings saying that some atoms are close to each
other but I guess Minimisation step will take care of it.
thanks for all the help.
Nitin
On 11/14/05, David A. Case <case_at_scripps.edu> wrote:
> 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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