---------- Forwarded message ----------
From: Dima A Sabbah <dsabbah.unmc.edu>
Date: Tue, Oct 5, 2010 at 11:30 AM
Subject: Fw: Re: [AMBER] NMR refinement in explicite water
To: dasabbah.gmav.unomaha.edu
Hello,
Let ntb =0
some systems can't be minimized by conjugate gradient; those are unstable or
complex.Therefore, if maxcyc = 1000, let ncyc =1000.
Hope it will work,
Dima
-----Forwarded by Dima A Sabbah/Students/UNMC/UNEBR on 10/05/2010 11:29AM
-----
To: AMBER Mailing List <amber.ambermd.org>
From: Dima A Sabbah/Students/UNMC/UNEBR
Date: 10/04/2010 09:25AM
Subject: Re: [AMBER] NMR refinement in explicite water
Hello,
Let ntb =0
some systems can't be minimized by conjugate gradient; those are unstable or
complex.Therefore, if maxcyc = 1000, let ncyc =1000.
Hope it will work,
Dima
-----Baptiste Legrand <bap.legrand.gmail.com> wrote: -----
To: AMBER Mailing List <amber.ambermd.org>
From: Baptiste Legrand <bap.legrand.gmail.com>
Date: 10/04/2010 09:13AM
Subject: Re: [AMBER] NMR refinement in explicite water
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 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
>>>
>>> _______________________________________________
>>> AMBER mailing list
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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--
Dima Sabbah
PhD Student
UNMC
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Received on Tue Oct 05 2010 - 10:00:03 PDT
