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?
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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Received on Thu Aug 11 2011 - 14:30:03 PDT
