AMBER Archive (2006)

Subject: Re: AMBER: xleap problem

From: Ilyas Yildirim (
Date: Wed Jun 07 2006 - 01:49:04 CDT

>From tleap:

> help saveamberprep

    saveAmberPrep unit filename

      UNIT _unit_
      STRING _filename_

Save all residues in the UNIT to a 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

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 <> 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)	-
  -			-

----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to