Dear DAC,
Thanks for your response. After a lot of hassle, I have decided to write a
perl script which creates the prepi file for the given structure. I just
needed to change the charges for the residues. So I wrote the
script such that the known .prepi file for the known residues (A,C,G,U
and their 3' and 5' end prepi files), the .pdb file of the structure and
the charge file which was created by using the given .pdb file (after
following the RESP procedure) are given in the command line, and it will
automatically create the modified .prepi file (only the charge column
will be different). Now when I load the .prepi structures in xleap, I
dont get any errors. Thanks for your time.
Best,
On Wed, 27 Jul 2005, David A. Case wrote:
> On Wed, Jul 27, 2005, Ilyas Yildirim wrote:
> >
> >
> > 'antechamber' assigns almost the correct atom type information
> > automatically, but the 4th column is different when compared with the
> > amber's library for those residues. (For A,C,G,and U) Do I have to change
> > those assigned LINK info to the ones in the AMBER database? If yes, is
> > there a quick way to do it?
> >
> > Best,
> >
> > PS: Example .prepi file
> >
> > RA which is automatically created by antechamber
> > ...
> > 4 O1P O2 M 3.487627 1.543250 0.125532 -0.792100
> > 5 P P M 2.394907 0.826000 0.819956 1.220980
> > 6 O2P O2 E 0.990655 1.042178 0.405519 -0.792100
> > 7 O5* OS M 2.703494 -0.752768 0.748009 -0.506960
> > ...
> >
> > In amber's database, the .prepi for RA is as follows:
> > ...
> > 4 P P M 2.314489 1.776673 -0.478436 1.166200
> > 5 O1P O2 E 1.933410 3.073374 -1.081549 -0.776000
> > 6 O2P O2 E 3.156547 0.871841 -1.292450 -0.776000
> > 7 O5' OS M 2.994369 2.142475 0.922974 -0.498900
> > ...
>
> You should modify what antechamber did to look like the Amber library:
> switch the order of atoms 4 and 5, and change the fourth column. Otherwise,
> you will have problems when you go to link this into a longer piece of RNA.
>
> Antechamber was originally designed to handle complete molecules, with no
> missing covalent connections. You have to be a little careful in using it
> to create residues that will later be linked into a polymer.
>
> ...good luck....dac
>
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>
--
Ilyas Yildirim
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Received on Thu Jul 28 2005 - 06:53:01 PDT
