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: Thu Nov 10 2005 - 10:40:21 CST

Dear Bill and Ilyas,
  Thanks for replying. I tried putting TER after every molecule. But
it did not work.
Ilyas, the file that I sent you was only one lipid. That can be loaded
without any erros. I am now attaching two such lipids that are next to
each other. This file called "popc.pdb" does not load and gives the
same error. I would appreciate if you could quickly load the file. You
would also need to load the following 'prepin' and frcmod files
(before loading the PDB file) by saying:

loadamberprep popc.prepin
loadamberparams popc.frcmod

If you do not load these files, Xleap (amber 8) wud load the PDB file
saying that any of the atoms are not in standard residue template.

Now, there is one more thing. All the above holds only when I load
force-fields by saying

source leaprc.ff99
and source leaprc.gaff.

If dont load these force-fields and only load the above prepin and
frcmod files, it loads the pdb but gives the following messages:
......
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-C73-C72-*
+--- With Sp0 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-C73-C74-*
+--- With Sp0 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-C73-C72-*
+--- With Sp0 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-C73-C74-*
+--- With Sp0 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
........

and so on.

After these messages, the PDB file (containing 2 lipids) is loaded.
When I say edit the PDB files, it connects the terminal carbon atoms
of the two lipids by a bond (terminal carbon atom of one lipid with
another terminal carbon atom of another lipid). There are TER entries
after each of the two molecules.

Any help wud be greatly appreciated.
Thanks a lot in advance,
Nitin

On 11/9/05, Ilyas Yildirim <yildirim_at_pas.rochester.edu> wrote:
> Hi Nitin,
>
> I could load the test.pdb file u sent in xleap. I did not get any error. I
> am using AMBER 8. Which version of AMBER are u using?
>
> On Wed, 9 Nov 2005, Nitin Bhardwaj wrote:
>
> > Dear All,
> > I have created the inpcrd and prmtop files a lipid molecule using
> > the antechamber. While doing this I used a single molecule. Everything
> > was fine.
> > Then I replicated the molecules to create a bilyer. When I load this
> > PDB file containing the bilayer, I get the following message:
> >
> > In file [chirality.c], line 121
> > !FATAL: Message: Atom C67 is not in the first list.
> > I tried to follow the program "chirality.c" but could not get it.
> > Have any of you seen this problem before? Please let me know if anyone
> > can suggest a solution to the problem?
> > I am attaching a copy of a single lipid if you wanna look at it.
> > Rgds,
> > Thanks,
> > Nitin
> >
>
> --
> Ilyas Yildirim
> ---------------------------------------------------------------
> - Department of Chemisty - -
> - University of Rochester - -
> - Hutchison Hall, # B10 - -
> - Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
> - http://www.pas.rochester.edu/~yildirim/ -
> ---------------------------------------------------------------
>
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