Re: [AMBER] NMR refinement in explicite water

From: Baptiste Legrand <bap.legrand.gmail.com>
Date: Thu, 07 Oct 2010 11:53:39 +0200

  Thanks Jason and Dima, these solutions work.
I continue to build my protocole following the example/tutorial
available here (or in the amber6 manual):
http://ambermd.org/doc6/html/AMBER-sh-4.3.html
But It seems that some parameters are obsolete for amber10. For example:

+--------------------------------------------------------+
  | Constant pressure equilibration |
  +--------------------------------------------------------+
  | |
  | Constant pressure simulation |
  | |
  |&cntrl |
  | imin=0, nmropt=1, ntx=7, irest=1, |
  | scee=1.2, cut=9.0, |
  | ntt=1, tempi=300., temp0=300.0, |
  | ntb=2, (constant pressure) |
  | ntp=2, (pressure regulation) |
  | ntc=2, tol=0.000001, |
  | ntpr=100, ntwr=99999, |
  | ntcm=1, nscm=1000, ndfmin=-3, |
  | ntr=1, |
  | nstlim=20000, |
  |&end |
  |&wt type='REST', istep1=0,istep2=1000,value1=1.0, |
  | value2=1.0,&end |
  |&wt type='END'&end |
  |LISTOUT=POUT |
  |DISANG=RST |
  |Group input for restrained atoms |
  | 5.0 |
  |RES 1 20 |
  |END |
  |END |
  +--------------------------------------------------------+

ntcm and ndfmin flags induce a error message and their definitions can't
be found in the amber10 manual but in the amber6 manual. Are they necessary?
Other errors should appear in the next steps of the tutorial, I have
checked for an update of this example for new amber versions but I don't
find it for the moment.
Thanks

Best regards,
Baptiste



Le 04/10/2010 16:49, Jason Swails a écrit :
> 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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Received on Thu Oct 07 2010 - 03:00:02 PDT
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