What about pres0=1,taup=1,ntp=1?
modify the input file and it will work.
On Thu, Oct 7, 2010 at 4:53 AM, Baptiste Legrand <bap.legrand.gmail.com>wrote:
> 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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--
Dima Sabbah
PhD Student
UNMC
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Received on Thu Oct 07 2010 - 07:00:05 PDT
