AMBER Archive (2006)

Subject: Re: AMBER: xleap problem

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Wed Jun 07 2006 - 09:22:12 CDT

Thank you.

If one doesn't know the existance of command 'saveamberprep',
how can he imagine to type 'help'?

Anyway, you can save prep.in file using antechamber.
If your residue name is unique, atom name doesn't matter.
Only in the residue, you can't use same atom name.

On 6/7/06, Ilyas Yildirim <yildirim_at_pas.rochester.edu> wrote:
> From tleap:
>
> > help saveamberprep
>
> saveAmberPrep unit filename
>
> UNIT _unit_
> STRING _filename_
>
> Save all residues in the UNIT to a prep.in file. All possible improper
> dihedrals are given for each residue, so unwanted ones need to be
> deleted from the file. 'Connect0' and 'connect1' atoms must be defined
> for each residue.
>
> Even though saveamberprep is not explained in the manual, u can get help
> from 'help <command name>' in tleap/xleap.
>
> For Hashem Taha's question; do the following to see if saveamberprep is
> working:
>
> Run xleap and,
> ------------------
> source leaprc.ff99
> saveamberprep RG rg.prep
> ------------------
> If this is working, that means that 'saveamberprep' command is working
> fine. In this case, I would say that your structure has some problem in
> it. Maybe there is a problem with atom naming. Without further info. I
> cannot say anything. But try the above test to see if saveamberprep is
> working fine or not.
>
> Good luck,
>
> On Tue, 6 Jun 2006, Myunggi Yi wrote:
>
> > There is no saveAmberPrep in "leap" command from the manual.
> > You may want to read "Antechamber" manual.
> >
> >
> > On 6/6/06, Hashem Taha <hashemt_at_gmail.com> wrote:
> > > i am trying to make prep file (from my pdb file) using xleap, but every time
> > > i try to use 'saveAmberPrep unit file.prep' xleap says that it's saving the
> > > prep file (saving prep, residue unit ...), but it just freezes at that point
> > > and crashes. I have tried doing this on several computers, all of which gave
> > > the same result. there were no errors in the unit after using 'check unit'
> > > and all the connect points were set properly. There were also no error
> > > messages given. I don't what is going on. any help is appreciated. the pdb
> > > file of the molecule i am using is attached if needed.
> > >
> > >
> >
> >
> >
>
> --
> Ilyas Yildirim
> ---------------------------------------------------------------
> - Department of Chemisty - -
> - University of Rochester - -
> - Hutchison Hall, # B10 - -
> - Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
> - http://www.pas.rochester.edu/~yildirim/ -
> ---------------------------------------------------------------
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> 

-- 
Best wishes,

MYUNGGI YI
==================================
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306

Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu