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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Received on Thu Sep 30 2010 - 11:00:12 PDT
