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: Fri Nov 11 2005 - 10:25:52 CST

Dear Ilyas,
  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 tried another thing. I loaded the PDB file containing only two
lipids with prepin and frcmod file (without ff99 and gaff). It gave me
messages about sp3-sp3-sp3 bonds as mentioned in my previous mail. And
I removed the bond in Xleap using the 'erase' option. Then I saved
that as a PDB file. I reloaded this as a PDB file to check if the bond
was there. It was not. So, I tried to create a new prepin file for
this pdb. But it gave error saying that MAX number of atoms has been
reached. I guess that's because there were two molecules of lipid in
that. So, I removed the second one and recreated the prepin file which
was fine. But even with this new prepin file, I can only load one
molecule. When I try to load file with 2 or more lipids, all of the
aforementioned errors hold.

I am at my wit's end.
Thanks a lot in advance.
Rgds,
Nitin

On 11/10/05, Ilyas Yildirim <yildirim_at_pas.rochester.edu> wrote:
> Dear Nitin,
>
> I think your popc.pdb and the popc.prepin files dont resemble the same
> structure(s). It is always giving an error for C67, even when C67 is not
> present in the structure. Are they too close to each one, the structures
> in popc.pdb? Your .prepin file is ok, it is giving all of the necessary
> atoms/atom types/connections for POP. But when I just keep the following
> info in your .pdb file
>
> ATOM 1 N POP 1 -9.538 10.243 11.841 1.00 0.00
> TER
> ATOM 135 N POP 2 -1.828 10.103 11.740 1.00 0.00
> TER
> END
>
> and try to load this structure, still I am getting the same error. I am
> thinking that your popc.pdb file has some problems in it.
>
> Good luck,
>
> PS: I dont think that u need a modified frcmod file for this structure.
>
> On Thu, 10 Nov 2005, Nitin Bhardwaj wrote:
>
> > 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/ -
> > > ---------------------------------------------------------------
> > >
> > > -----------------------------------------------------------------------
> > > The AMBER Mail Reflector
> > > To post, send mail to amber_at_scripps.edu
> > > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> > >
> >
>
> --
> 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/ -
> ---------------------------------------------------------------
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu