Dear All,
I have a question regarding xleap. It is about the AMBER's libraries, and
something strange is happening when I am trying to do the following:
I start 'xleap'. Then;
> source leaprc.ff99
> savepdb RC rc.pdb
> quit
Now, I see the file 'rc.pdb' in the directory. Then I start 'xleap' again;
> source leaprc.ff99
> molecule = loadpdb rc.pdb
and xleap adds 2 atoms!!! Here is what xleap is giving me after I load the
rc.pdb:
> molecule = loadpdb rc.pdb
Loading PDB file: ./rc.pdb
Created a new atom named: O2* within residue: .R<RC 1>
Created a new atom named: HO*2 within residue: .R<RC 1>
Added missing heavy atom: .R<RC 1>.A<O2' 29>
total atoms in file: 31
Leap added 2 missing atoms according to residue templates:
1 Heavy
1 H / lone pairs
The file contained 2 atoms not in residue templates
Since added/missing = extra, there is a high probability
of atoms with 'incorrect' names; you may want to
use addPdbAtomMap to map these names, or change in file
Question: I have saved the .pdb structure according to the AMBER' residue
library, and when I try to open the same .pdb in xleap, it adds two atoms
(saying that they are missing, even though they are not!). Am I missing
something here? Thanks in advance for your responses.
Best,
--
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 Thu May 12 2005 - 03:52:59 PDT
