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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Received on Thu Sep 30 2010 - 05:00:07 PDT
