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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Received on Wed Jul 27 2005 - 16:53:00 PDT
