AMBER Archive (2005)

Subject: Re: AMBER: Problem with xleap

From: JunJun Liu (ljjlp03_at_gmail.com)
Date: Thu May 12 2005 - 02:19:24 CDT


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_at_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 ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu