Hello,
Thanks for the replies so far.
I figured that residues 1 thru 'n' have to be placed exactly in that order
in the .pdb file for leap to work properly (took me a while to recognize
this feature different from other simulation programs). So, now, I load the
leaprc.ffo2, followed by my nh2.lib (I renamed it to nh2_lib to attach
here), and then my .pdb file, and things look much better (?) :
> APN = loadpdb ambertrans1.pdb
Loading PDB file: ./ambertrans1.pdb
One sided connection. Residue: missing connect0 atom.
total atoms in file: 23
(What could this mean?)
Then, I do:
> bond APN.2.C APN.3.N
and then,
> check APN which gives,
Checking 'APN'....
Checking parameters for unit 'APN'.
Checking for bond parameters.
Could not find bond parameter for: C - N3
Checking for angle parameters.
Could not find angle parameter: O - C - N3
Could not find angle parameter: C - N3 - H
Could not find angle parameter: C - N3 - H
Could not find angle parameter: CT - C - N3
There are missing parameters.
Unit is OK.
Could you please tell me how to add the missing parameters at this point?
I am attaching my nh2.lib and my full pdb file (ambertrans1.pdb) herewith.
Thanks,
Neelanjana
On 7/17/07, David A. Case <case.scripps.edu> wrote:
>
> On Tue, Jul 17, 2007, Neelanjana Sengupta wrote:
>
> > This is again regarding AcProNH2 (acetyl proline amide).
> >
> > Now I have successfully made a .lib file for my NH2 residue, and
> numbered
> > and renamed my .pdb file to have ACE (res#1), PRO (res#2) and NH2
> (res#3).
> > When I load leaprc.ff02 followed by my nh2.lib into Leap, everything
> looks
> > OK.
> >
> > The issues:
> > 1) When I next load my .pdb file, Leap still adds an O- to the PROline,
> > thinking it to be the last residue:
> > Added missing heavy atom: .R<CPRO 5>.A<OXT 15>
>
> I think you will have to post your pdb file...it's not clear without that
> why LEaP thinks that the proline is a C-terminal residue.
>
> Also, try making ACE-PRO-NME, with the standard NME residue. If that
> works,
> you can look for the differences between NME and your NH2 residue (other
> than
> the missing methyl group!) that might explain the different behavior.
>
> ...good luck...dac
>
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- application/octet-stream attachment: nh2_lib
Received on Wed Jul 18 2007 - 06:07:48 PDT
