Thanks!
I manually edited the inpcrd file with the last line of an old file that
worked. I should probably double check everything again.
I see only 3 angles specified, is this correct for a box?
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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Received on Thu Aug 11 2011 - 14:00:03 PDT
