is there an option to remove the water molecules from the
structure files?
Are you going to do MD in gaeseous phase? if yes, you can remove water.
Do leap recognize this atom type to generate the inpcrd and prmtop files (or
may
be we should use the n.3)?
Yes, leap recognize the quaternary nitrogen, have you seen gaff.dat file in
Amber source?
You can assign the atom type based on this file.
Good luck!
Dima
On Thu, Oct 7, 2010 at 9:15 AM, Baptiste Legrand <bap.legrand.gmail.com>wrote:
> Ok thanks, I'm going to try with these parameters. Indeed, the rest of
> the tutorial works very well with amber10.
> At the end, is there an option to remove the water molecules from the
> structure files?
> I have a last question about the Nterminal of peptides. Classically the
> NH3+ in the mol2 format is indicated by a n.4 atom type. Do leap
> recognize this atom type to generate the inpcrd and prmtop files (or may
> be we should use the n.3)?
>
> Best regards,
> Baptiste
>
>
> Le 07/10/2010 15:55, Sabbah, Dima a écrit :
> > 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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> >>>>>>
> >>>>> _______________________________________________
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> >>>>
> >>>
> >>
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> >>
> >
> >
>
>
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--
Dima Sabbah
PhD Student
UNMC
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Received on Thu Oct 07 2010 - 08:00:03 PDT
