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.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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>
--
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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Received on Fri Nov 11 2005 - 02:53:00 PST
