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 - 11:13:33 CST

David,
     I am using Amber 8 on Windows XP. After your mail I tried to do
the whole thing all over again.

First loaded the prepin and frcmod files only (without loading the
gaff) and then loaded the PDB. It gives a whole list of errors :

.......
+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
................

when I edited the PDB, I can still see the bond between the two lipids.

Then I loaded the gaff and tried to load the PDB file. But it died saying:

In file [chirality.c], line 121
!FATAL: Message: Atom C67 is not in the first list.

Can you tell me if you did any thing diferent from what I said above.
Its strange that the same software behaves so differently with the
same set of files.

Thanks for replying.
Rgds,
Nitin
On 11/10/05, David A. Case <case_at_scripps.edu> wrote:
> On Thu, Nov 10, 2005, Nitin Bhardwaj wrote:
> >
> > 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.
>
> Doesn't happen for me...everything looks fine, and there are no bonds between
> the two lipids. Did you say which version of Amber you are using? What
> operating system and compiler are you using?
>
> ...dac
>
> -----------------------------------------------------------------------
> 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