2010/6/20 Catein Catherine <askamber23.hotmail.com>
>
> Dear Jason and amber fans,
>
>
>
> Thanks for your comments. Is AmberTools 1.4 compatible with AMBER 10?
>
Yes. sander/pmemd will run MD using any topology file, no matter how it's
created (as long as it's a valid prmtop). A notable exception is variable
1-4 scaling, which was added to the prmtop file for AmberTools 1.4, and is
not recognized in amber10 (amber10 doesn't know what to do with variable 1-4
scaling). However, you need to extract AmberTools 1.4 into the amber11
directory, do not try to put it in the same directory as amber10.
>
>
>
> I have a system with both DNA and protein, should I call up both ff99SB and
> ff99bsc.0?
>
ff99bsc0 loads all the ff99SB parameters by default, so you only need
leaprc.ff99bsc0 (note there is no period before the 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!
>
You can either use the source command (source leaprc.ff99bsc0) in the xleap
window, or invoke xleap with
xleap -f leaprc.ff99bsc0
Both should work.
Good luck!
Jason
>
>
>
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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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 - 10:00:05 PDT
