Hello,
On Mon, Oct 4, 2010 at 10:13 AM, Baptiste Legrand <bap.legrand.gmail.com>wrote:
> Thanks Daniel, now the script works very well.
> I have an error message and high energies during the initial
> minimization for the water molecule and the counterions, in the min.out
> file:
>
> RESTARTED DUE TO LINMIN FAILURE
>
This occurs because the line search fails to find the "right" direction to
continue minimizing. If you've reached this point, MD should proceed just
fine. If you're looking to really minimize past this, consider using the
xmin minimizer -- ntmin=3 if I'm not mistaken. See details in the amber
manual. It's a better minimization routine than the default.
Good luck!
Jason
>
> This message seems to commonly occur, I'm going to look at this.
> Baptiste
>
>
> Le 30/09/2010 19:57, Daniel Roe a écrit :
> > You can create your tleap file on the fly using 'cat' and a redirector,
> e.g.:
> >
> > cat> leap.in<<EOF
> > source leaprc.ff99sb
> > loadamberprep ./sa/JMV4590_vac_$x.prepin
> > ...
> > quit
> > EOF
> >
> > -Dan
> >
> >
> > On Thu, Sep 30, 2010 at 7:55 AM, Baptiste Legrand<bap.legrand.gmail.com>
> wrote:
> >> Thanks Daniel,
> >> I have started to create a little script. I run this file to
> >> automatically prepare my files and run sander for the minimization, SA
> >> etc...
> >>
> >> #Starting from the 10 structures refine in vacuum with NMR restraints, I
> >> generate prepin files to feed leap with each file (I don't know if it is
> >> the best way):
> >> ...
> >> for x in `seq 1 10`
> >> do
> >> antechamber -i ./sa/JMV4590_vac_$x.pdb -fi pdb -o
> >> ./sa/JMV4590_vac_$x.prepin -fo prepi -c bcc -s 2 -nc 1
> >> parmchk -i ./sa/JMV4590_vac_$x.prepin -f prepi -o
> ./sa/JMV4590_vac_$x.frcmod
> >>
> >> #Then I run leap using the file JMV4590_wat.leap. This manner works for
> >> one file if I replace the $x by a number but I don't know how to
> >> increment the 10 files with the $x variable.
> >> tleap -f JMV4590_wat.leap
> >> done
> >> ...
> >>
> >> The JMV4590_wat.leap file:
> >> source leaprc.gaff
> >> source leaprc.ff99SB
> >> loadamberprep ./sa/JMV4590_vac_$x.prepin
> >> loadamberparams ./sa/JMV4590_vac_$x.frcmod
> >> addions UNK Cl- 0
> >> solvatebox UNK TIP3PBOX 12 0.75
> >> saveamberparm UNK ./wat/JMV4590_vac_$x.prmtop
> ./wat/JMV4590_vac_$x.inpcrd
> >> quit
> >>
> >> What is the good manner to do this? Thanks
> >>
> >> Baptiste
> >>
> >>
> >>
> >>
> >>
> >> Le 29/09/2010 16:54, Daniel Roe a écrit :
> >>> On Wed, Sep 29, 2010 at 9:15 AM, Baptiste Legrand<
> bap.legrand.gmail.com> wrote:
> >>>> How can I ask leap to automatically take each structure and create
> >>>> parameter and coordinate files? What is the best way to link the steps
> >>>> in vacuum and the final refinement in water? Thanks.
> >>> You can run tleap in an automated way (e.g. from a script) using the
> >>> '-f' option. Assuming the file leap.in contains all the commands you
> >>> want to run,
> >>>
> >>> tleap -f leap.in
> >>>
> >>> should get you what you want. I recommend you redirect the output to a
> >>> file and check this for any problems (errors, warnings, etc). Also
> >>> make sure you add a 'quit' command at the end of your leap.in file so
> >>> leap terminates properly.
> >>>
> >>> -Dan
> >>>
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> >>
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>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Oct 04 2010 - 08:00:03 PDT
