On Thu, Aug 11, 2011 at 5:07 PM, David Cantu <cantudav.amber.gmail.com>wrote:
> I found this on ambermd.org/formats about the prmtop file.
>
> %FLAG BOX_DIMENSIONS
> %FORMAT(5E16.8) OLDBETA, BOX(1), BOX(2), BOX(3)
> OLDBETA : periodic box, angle between the XY and YZ planes in
> degrees. This is now redundant, as it is present in the
> inpcrd files. It is ignored here.
> BOX : the periodic box lengths in the X, Y, and Z directions.
> This is now redundant, as it is present in the inpcrd files.
> It is ignored here.
>
>
> Is this current with AmberTools 1.4 and Amber11?
>
Yes. I updated the prmtop specification recently (within the last year as I
recall). There's also a pointer in the POINTERS section, IFBOX, that is set
based on what kind of (if any) box exists. 0 for no box, 1 for orthogonal,
2 for non-orthogonal (like truncated octahedron).
The prmtop format doesn't change very much, and excluding the extraneous
CHARMM-specific sections written by chamber (and other sections added by
other programs, like addles, the HCP section, etc.), this is up-to-date
AFAIK.
HTH,
Jason
>
> David
>
>
> On Thu, Aug 11, 2011 at 4:03 PM, David Cantu <cantudav.amber.gmail.com
> >wrote:
>
> > Hi Dan,
> >
> > We have to do some edits on the molecule on Xleap. The first time we went
> > through it, we did the solvatebox command. Then we saved a pdb and prmtop
> > and inpcrd. These worked.
> >
> > Then we realized that we forgot to edit something. We opened the PDB
> > (solvated), edited the file. We did not run the solvatebox command again
> as
> > we already had the system with waters. Then made neew prmtop and inpcrd
> > (these did not work).
> >
> > My guess is that because we did not run the solvatebox command the
> second,
> > no box was done. I just copied the last line from the 1st inpcrd into the
> > 2nd.
> >
> > Is there also box info on the prmtop file?
> >
> > David
> >
> >
> > On Thu, Aug 11, 2011 at 3:53 PM, Daniel Roe <daniel.r.roe.gmail.com
> >wrote:
> >
> >> Hi,
> >>
> >> On Thu, Aug 11, 2011 at 4:37 PM, David Cantu <cantudav.amber.gmail.com>
> >> wrote:
> >> > I manually edited the inpcrd file with the last line of an old file
> that
> >> > worked. I should probably double check everything again.
> >>
> >> You shouldn't have to manually edit your inpcrd or topology files to
> >> introduce box information. If you're not careful you could create
> >> serious problems with your simulation (e.g. if you specify a box
> >> that's too small or something). If you're using the solvatebox or
> >> solvateoct commands the box info should be there - if it's not please
> >> post the exact commands you are using so we can attempt to reproduce
> >> this behavior.
> >>
> >> >
> >> > I see only 3 angles specified, is this correct for a box?
> >>
> >> If you only see three numbers at the end of your restart these are
> >> lengths, not angles, and I believe this is correct for an orthogonal
> >> box only. When box angles (the last 3 numbers on the box line) are not
> >> present in the restart file, sander (and I assume pmemd) sets them to
> >> 90. If you have a non-orthogonal box like truncated octahedron, the
> >> angles should be in the restart file.
> >>
> >> -Dan
> >>
> >> >
> >> > David
> >> >
> >> > On Thu, Aug 11, 2011 at 3:32 PM, Carlos Simmerling <
> >> > carlos.simmerling.gmail.com> wrote:
> >> >
> >> >> yes, dimensions and angles
> >> >>
> >> >>
> >> >>
> >> >> On Thu, Aug 11, 2011 at 4:23 PM, David Cantu <
> cantudav.amber.gmail.com
> >> >
> >> >> wrote:
> >> >> > A quick question about inpcrd files:
> >> >> >
> >> >> > These are the two final lines of an inpcrd file that worked:
> >> >> >
> >> >> > 13.2486240 12.8955690 15.7921610
> >> >> > 125.2696010 120.1799690 106.9524940 90.0000000 90.0000000
> >> 90.0000000
> >> >> >
> >> >> > Is the last line of numbers the box specifications?
> >> >> >
> >> >> > Thanks,
> >> >> >
> >> >> > David
> >> >> >
> >> >> > On Thu, Aug 11, 2011 at 2:35 PM, David Cantu <
> >> cantudav.amber.gmail.com
> >> >> >wrote:
> >> >> >
> >> >> >> We had to do many changes to the molecules in Xleap. We dont have
> a
> >> >> >> leap.in file.
> >> >> >>
> >> >> >> Thanks again for all the help, we'll try to load everything into
> >> Xleap
> >> >> >> again.
> >> >> >>
> >> >> >> I will make a leap.in file in case we do have the same problem
> >> again.
> >> >> >>
> >> >> >> Thanks,
> >> >> >>
> >> >> >> David
> >> >> >>
> >> >> >>
> >> >> >> On Thu, Aug 11, 2011 at 1:12 PM, Daniel Roe <
> daniel.r.roe.gmail.com
> >> >> >wrote:
> >> >> >>
> >> >> >>> It appears your restart does not contain box information. Can you
> >> >> >>> please post your entire leap input?
> >> >> >>>
> >> >> >>> -Dan
> >> >> >>>
> >> >> >>> On Thu, Aug 11, 2011 at 1:48 PM, David Cantu <
> >> cantudav.amber.gmail.com
> >> >> >
> >> >> >>> wrote:
> >> >> >>> > I used TIP3PBOX
> >> >> >>> >
> >> >> >>> > I do not see any BOX INFO. Here is the end of the inpcrd file:
> >> >> >>> >
> >> >> >>> > [dcantu.lightningsmp julie_prob]$ tail acds.inpcrd
> >> >> >>> > 14.8590000 11.6010000 11.1070000 13.1510000 12.8680000
> >> >> 7.9920000
> >> >> >>> > 12.6910000 13.6200000 7.6180000 12.5220000 12.1490000
> >> >> 7.9330000
> >> >> >>> > 3.5810000 11.1770000 7.1670000 4.0970000 10.5660000
> >> >> 6.6420000
> >> >> >>> > 4.2310000 11.6800000 7.6580000 6.3200000 12.0680000
> >> >> 7.9940000
> >> >> >>> > 6.6080000 11.8130000 7.1170000 6.8330000 11.5160000
> >> >> 8.5840000
> >> >> >>> > 6.3880000 12.9900000 15.3600000 7.3140000 12.7540000
> >> >> 15.4040000
> >> >> >>> > 6.3730000 13.8170000 14.8790000 14.6220000 12.5320000
> >> >> 2.3580000
> >> >> >>> > 14.7970000 11.8460000 1.7140000 13.9240000 13.0570000
> >> >> 1.9660000
> >> >> >>> > 12.9550000 12.2170000 15.1850000 13.7480000 11.7210000
> >> >> 14.9770000
> >> >> >>> > 13.2490000 12.8960000 15.7920000
> >> >> >>> >
> >> >> >>> >
> >> >> >>> > Thanks,
> >> >> >>> >
> >> >> >>> > David
> >> >> >>> >
> >> >> >>> >
> >> >> >>> > On Thu, Aug 11, 2011 at 12:30 PM, Bill Ross <ross.cgl.ucsf.edu
> >
> >> >> wrote:
> >> >> >>> >
> >> >> >>> >> > I made the inpcrd on Xleap, after solvating a protein.
> >> >> >>> >>
> >> >> >>> >> What solvate cmd did you use? Do you see box info if you 'tail
> >> >> inpcrd'?
> >> >> >>> >>
> >> >> >>> >> Bill
> >> >> >>> >>
> >> >> >>> >> _______________________________________________
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> >> >> >>>
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> >> >> >>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Aug 11 2011 - 14:30:06 PDT
