Re: [AMBER] Inpcrd file problem

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Thu, 11 Aug 2011 16:53:11 -0400

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
>> >>> >>
>> >>> >> _______________________________________________
>> >>> >> AMBER mailing list
>> >>> >> AMBER.ambermd.org
>> >>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>> >>
>> >>> > _______________________________________________
>> >>> > AMBER mailing list
>> >>> > AMBER.ambermd.org
>> >>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >>> >
>> >>>
>> >>> _______________________________________________
>> >>> AMBER mailing list
>> >>> AMBER.ambermd.org
>> >>> http://lists.ambermd.org/mailman/listinfo/amber
>> >>>
>> >>
>> >>
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 11 2011 - 14:00:04 PDT
Custom Search