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
Received on Thu Aug 11 2011 - 14:00:02 PDT
