leaprc.f99 is for mapping DNA. In your case, you can try "source
leaprc.rna.ff99" instead of leaprc.ff99.
Regards!
Liu
On Thu, 12 May 2005 09:45:50 +0800, Ilyas Yildirim
<yildirim.pas.rochester.edu> wrote:
> 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,
>
--
JunJun Liu
College of Chemistry
Central China Normal University
WuHan 430079
P.R. China
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Received on Thu May 12 2005 - 08:53:02 PDT
