I that out 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, 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.
On 7/17/07, David A. Case <case.scripps.edu> wrote:
> 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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--
****************************************
Neelanjana Sengupta, PhD student
Dept. of Chemistry
Univ. of California-Irvine
Irvine, CA 92697
USA
Phone: 1-949-824 9921
email: sengupta.uci.edu
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Received on Wed Jul 18 2007 - 06:07:48 PDT
