Dear Jason and amber fans,
Thanks for your comments. Is AmberTools 1.4 compatible with AMBER 10?
I have a system with both DNA and protein, should I call up both ff99SB and ff99bsc.0?
How can I call up the ff99bsc.0? Should I type "source leaprc.ff99bsc.0" in the xleap window? Or should I call up the xleap window using other command lines? Thanks a lot!
Best regards,
Cat
> Date: Sun, 20 Jun 2010 12:06:17 -0400
> From: jason.swails.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] xleap problem for terminal DNA base pairs.
>
> Hello,
>
> Try using AmberTools 1.4 instead of 1.2. If I recall recent responses on
> the list correctly, the PDB standard has changed between the releases of
> AmberTools 1.4 and AmberTools 1.2. Therefore, you'll probably have better
> luck with AmberTools 1.4. Moreover, I think you should be using
> leaprc.ff99bsc0 for nucleic acids instead of ff99SB.
>
> Good luck!
> Jason
>
> On Sun, Jun 20, 2010 at 11:56 AM, Catein Catherine
> <askamber23.hotmail.com>wrote:
>
> >
> > Dear Amber users,
> >
> >
> >
> > I have compiled ambertool 1.2 and amber10 on ubunta 10.1.
> >
> >
> >
> > I used a pdb file with a DNA strand with 22-base pairs. Using following
> > commands
> >
> >
> >
> > $AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
> >
> >
> >
> > However, I found all the terminal residues's PO2 atoms cannot be recongized
> > by the program. I double checked the name of the atoms in my pdb file. For
> > example the first base pairs is named as DA, where the PO2 atom name are as
> > follows P and O1P and O2P. They should be recongizable in xleap.
> > Similarly, I found the residue A in the middle of the DNA are using the same
> > names, and able to be recongized by xleap.
> >
> >
> >
> > Could you mind to help if I have used the wrong naming system for terminal
> > residues?
> >
> >
> >
> > Best regards,
> >
> >
> >
> > Cat
> >
> >
> >
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>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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Received on Sun Jun 20 2010 - 09:30:06 PDT
