I forgot to examine the cap of solvent in xleap. Now, how are inpcrd rest mdcrd
files to be handled with VMD? This question because I am now trying to
visualize the solute and cap with VMD. No problem for inpcrd and rst, though
the solute is completely out of the spherical assembly of TIP3PBOX. On
resizing, the solute is not resized.
With mdcrd there is a further problem, I believe a wrong choice of filetype
because the solute molecule is highly distorted with all options I tried.
To make the cap I used
solvateCap EQE TIP3PBOX {1.2 59.9 130.3} 20.0
where the cartesian coordinates for a central carbon atom in the solute were
taken from the prepin file from antechamber.
Does any shift of coordinates occur after the stage of prepin?
If all that is not clear, I have to change option to define the "position",
perhaps one that Ross suggested.
Thanks
francesco
--- "M. L. Dodson" <mldodson.houston.rr.com> wrote:
> Francesco Pietra wrote:
> > Hi Bud and Ross:
> > Thanks
> >
> > When launching the preliminary minimization with adjusted
> >
> > Initial min for qmmm with dftb
> > &cntrl
> > imin=1, maxcyc=500, ncyc=200,
> > cut=20.0, ntb=0, ntc=2, ntf=2,
> > ivcap=0, fcap=10, igb=10,
> > ifqnt=1
> > /
> > &qmmm
> > qmmask=':1',
> > qmcharge=0,
> > qmtheory=7,
> > qmshake=0,
> > qm_ewald=0
> > /
> >
> >
> > sander bombed. min_qmmm_dftb.out ended with:
> >
> > LOADING THE QUANTUM ATOMS AS GROUPS
> > Mask :1; matches 98 atoms
> > SANDER BOMB in subroutine read_qmmm_namelist
> > qmtheory = DFTB but qmgb > 1. DFTB does not currently
> > support full QM GB. Only qmgb values of 0 or 1 are supported.
> >
> >
> > Once flag "qmgb=0" is added just after "qmtheory=7", the minimization
> is going
> > on. From tail -f it is at NSTEP 50.
> >
> > I was unable to detect where GB is stated in the minin. I also wonder
> about the
> > difference between "qmgb=0" and qmgb=1" which I did not fin in either
> Amber9
> > manual or the pdf included in Marcus Elnster files.
> >
> > If there is nothing wrong about GB statements, I assume that qmgb=0
> (or qmgb=1)
> > flag should also be added to mdin, modified (for a trial) as follows
> >
> > 300K constant temp for qmmd with dftb
> > &cntrl
> > imin=0, ntb=0
> > cut=20.0, ntc=2, ntf=2,
> > tempi=300.0, temp0=300.0,
> > ntt=3, gamma_ln=1.0,
> > nstlim=1000, dt=0.002,
> > ivcap=0, fcap=10, igb=10
> > ntpr=10, ntwx=10,ifqnt=1
> > /
> > &qmmm
> > qmmask=':1',
> > qmcharge=0,
> > qmtheory=7,
> > qmgb=0,
> > qmshake=0,
> > qm_ewald=0
> > /
> >
> >
> >
> >
> > Thanks
> >
> > francesco
> >
>
> I'm sorry, my bad. I forgot that QMMM in amber9 does not support
> GB, either. You will not be able to use igb=10. (That is what
> specifies a GB simulation.)
>
> Bud
>
> >
> >
> > --- "M. L. Dodson" <mldodson.houston.rr.com> wrote:
> >
> >> Francesco Pietra wrote:
> >>> I am trying to build prmtop and inpcrd for qm-mm with theory=7
> (dftb). I am
> >>> stuck at solvateCap, argument #3 (position).
> >>>
> >>> Using *.prepin and *frcmod from previous successful runs with theory=2,
> >>>
> >>> startx
> >>>
> >>> $AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmod/leaprc.ff99
> >>>
> >>> source leaprc.gaff
> >>>
> >>> loadamberprep EQE.prepin
> >>>
> >>> loadamberparams EQE.frcmod
> >>>
> >>> check EQE (unit is OK)
> >>>
> >>> solvateCap EQE TIP3PBOX EQE 20.0
> >>>
> >>> returns
> >>>
> >>> Argument #3 is type Unit must be of type: [molecule residue atom list]
> >>>
> >>> Using as Argument #3: "1" (residue number in prepin), "C17" (a central
> >> carbon
> >>> atom number in prepin, "c" the C17 atom type, or, finally (and blindly)
> >>> EQE.2.CA the error is: Argument #3 is type String.
> >>>
> >>> I am short of imagination (even consulting the manual and the
> mailing list)
> >> of
> >>> what should be given in my case as Argument #3.
> >> Without getting into the structured design of LEaP, perhaps the
> >> easiest way to for you to proceed is to pick the atom you want to
> >> make the center of your spherical cap. For purposes of
> >> illustration, let us assume the Cartesian coordinates of that
> >> atom are:
> >>
> >> x = 1.0, y = 2.0, z = 3.0
> >>
> >> Then a solvate cap command using these coordinates might be:
> >>
> >> solvateCap EQE TIP3PBOX {1.0 2.0 3.0} 20.0
> >>
> >> The desc command is your friend when trying to learn the syntax of
> >> LEaP. You just have to practice.
> >>
> >>> ________________--
> >>> That said, on summing up info from the manual and suggestions from
> Bud and
> >>> Gustavo, I have a number of doubts about min.in and md.in, in
> particular
> >> if
> >>> qm_pme should be omitted at all. The two files I have set up read:
> >>>
> >>> Initial min for qmmm with dftb
> >>> &cntrl
> >>> imin=1, maxcyc=500, ncyc=200,
> >>> cut=20.0, ntb=1, ntc=2, ntf=2,
> >>> ivcap=0, fcap=10
> >>> ifqnt=1
> >>> /
> >>> &qmmm
> >>> qmmask=':1',
> >>> qmcharge=0,
> >>> qmtheory=7,
> >>> qmshake=0,
> >>> qm_ewald=0
> >>> /
> >>>
> >>> 300K constant temp for qmmd with dftb
> >>> &cntrl
> >>> imin=0, ntb=1
> >>> cut=20.0, ntc=2, ntf=2,
> >>> tempi=300.0, temp0=300.0,
> >>> ntt=3, gamma_ln=1.0,
> >>> nstlim=20000, dt=0.002,
> >>> ivcap=0, fcap=10,
> >>> ntpr=100, ntwx=100,ifqnt=1
> >>> /
> >>> &qmmm
> >>> qmmask=':1',
> >>> qmcharge=0,
> >>> qmtheory=7,
> >>> qmshake=0,
> >>> qm_ewald=0
> >>> /
> >>>
> >>>
> >>> I want to try if, at the current implementation of qm-mmm/dftb
> >>> in Amber9, speed is acceptable for a 98-atoms molecule. If
> >>> acceptable, to compare ESCF and EPtot with AM1.
> >>>
> >> Since amber9 sander cannot do pme with QMMM and qmtheory=7, you
> >> should not turn on qm_pme. Also, for solvent cap simulations,
> >> ntb=0, not ntb=1 as you have specified. And you should think
> >> about the suggestion on page 99 of the manual to set igb=10. I
> >> also think you may have to reduce the timestep. I use 0.5fs for
> >> QMMM steered MD, but you may be able to get by with 1.0fs, 2.0fs
> >> is generally workable, but is said to be borderline for classical
> >> MD. See the email list archives.
> >>
> >> Of course the definition of acceptable speed is personal, but I
> >> have found 90+ atom QM regions to be workable with qmtheory=7.
> >>
> >>>
> >>> Thanks for checking
> >>>
> >>> francesco pietra
> >> HTH,
> >>
> >> Bud Dodson
> >> --
> >> M. L. Dodson
> >> Email: mldodson-at-houston-dot-rr-dot-com
> >> Phone: eight_three_two-five_63-386_one
> >> -----------------------------------------------------------------------
> >> The AMBER Mail Reflector
> >> To post, send mail to amber.scripps.edu
> >> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >>
> >
> >
> >
> >
> >
>
____________________________________________________________________________________
> > Be a better Globetrotter. Get better travel answers from someone who
> knows. Yahoo! Answers - Check it out.
> > http://answers.yahoo.com/dir/?link=list&sid=396545469
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
>
> --
> M. L. Dodson
> Email: mldodson-at-houston-dot-rr-dot-com
> Phone: eight_three_two-56_three-386_one
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
____________________________________________________________________________________
Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s user panel and lay it on us.
http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Aug 26 2007 - 06:07:45 PDT
