AMBER Archive (2009)

Subject: Re: Re: [AMBER] read substrate into leap

From: Jason Swails (jason.swails_at_gmail.com)
Date: Wed Nov 18 2009 - 19:35:37 CST

Leap will only recognize residues that it is told about in library files.
When you source leaprc.ff___, it loads OFF libraries that contain the names
of all common residues (and their structures and attributes). Thus, if your
substrate residue is not one of the common amino acids (or nucleic acids),
you will likely need to create your own 'custom' residue. There are
tutorials that will walk you through this process on the amber tutorial
webpage here: http://ambermd.org/tutorials/ . Tutorials B4 and A1 and
A1.old will likely provide all the help you'll need to do this.

Good luck!
Jason

2009/11/18 sculiujl <sculiujl_at_163.com>

> HI Jason,
> Thank you for your help.I do as your advise.However,the leap programm
> cannot recongnize the residue name of substrate.
>
>
>
>
> 在2009-11-19，"Jason Swails" <jason.swails_at_gmail.com> 写道：
> >Hello,
> >
> >When you use the loadpdb command in leap, it loads the coordinates
> >automatically. For example
> >
> >l = loadpdb PDBFILE
> >
> >will load all of the atom types, atom names, and coordinates in PDBFILE in
> >unit "l".
> >
> >The short version: coordinates are read in with the PDB file, you don't
> have
> >to do anything extra.
> >
> >I hope this helps,
> >Jason
> >
> >2009/11/18 sculiujl <sculiujl_at_163.com>
> >
> >>
> >>
> >> HI amber users,
> >> I have a pdb file which contains the substrate .But I do not know how to
> >> read the coordinates of substrate into leap.
> >> Thank you in advance.
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER_at_ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >
> >
> >--
> >---------------------------------------
> >Jason M. Swails
> >Quantum Theory Project,
> >University of Florida
> >Ph.D. Graduate Student
> >352-392-4032
> >_______________________________________________
> >AMBER mailing list
> >AMBER_at_ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> 

-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber