Thanks a lot for all your help. The problem was solved by copying
manually the coordinates from the restrt to the incprd file.
On 8/20/2010 12:49 PM, Jason Swails wrote:
> Hi Arik,
>
> Writing the PDB will most likely get rid of the box information I think.
> Why not trajout individual restart files instead of pdbs? Is there a reason
> you save a slew of PDB files? If you trajout directly to restart files I
> think it should save the box info.
>
> Your inpcrd file has lost its formatting in the email. Is there a line with
> box information (3 numbers) at the very end? Make sure these are not
> coordinates. You can check how many lines there should be just based on the
> number of atoms in your system and given the fact that each atom has 3
> coordinates.
>
> Good luck!
> Jason
>
> On Fri, Aug 20, 2010 at 3:43 PM, arikcohen<arikcohen.ucla.edu> wrote:
>
>> Hi Jason,
>>
>> Thanks a lot for tour ultrafast replay and above all your help.
>>
>> 1. The files that I'm using are the pdb which were taken via ptraj using
>> the following command:
>>
>> trajin 1GTH_MD1.binpos 500 750 50
>> trajout HG2.pdb pdb
>> image familiar center
>> go
>>
>> 2. The system is solvated with a box of TIP3P, 10 A around the protein.
>>
>> 3. The last couple of lines of my inpcrd file (taken again via ptraj)are
>> as follows:
>>
>> 63.981 67.718 26.200 35.536 66.108 14.227 35.855 65.206
>> 14.246 35.298
>> 66.259 13.312 62.293 39.765 67.140 61.443 39.645 67.563
>> 62.912 39.842
>> 67.865 46.539 22.065 73.776 46.036 22.786 74.154 45.902
>> 21.576 73.255
>> 39.960 6.413 61.241 39.472 6.127 62.014 39.646 7.301 61.074
>> 77.810 77.810 77.810
>>
>>
>> Thanks a lot !!! again and all the best,
>>
>> Arik
>> On 8/20/2010 4:31 AM, Jason Swails wrote:
>>> Hello,
>>>
>>> Ptraj should not kill the box information without the keyword "nobox" at
>> the
>>> end of the trajout statement, to my understanding.
>>>
>>> What input file are you using? Is your system solvated? Should there be
>>> box information? What do the last couple lines of your inpcrd file look
>>> like?
>>>
>>> All the best,
>>> Jason
>>>
>>> On Thu, Aug 19, 2010 at 8:35 PM, arikcohen<arikcohen.ucla.edu> wrote:
>>>
>>>> Dear Amber users,
>>>>
>>>> I would be most thankful for your help in the following problem: I'm
>>>> trying to minimize snapshots(taken with ptraj) from a MD trajectory.
>>>> However when doing so, I'm encountering the following error:
>>>>
>>>> Flags: MPI
>>>> getting new box info from bottom of inpcrd
>>>> | INFO: Old style inpcrd file read
>>>>
>>>> | peek_ewald_inpcrd: Box info not found in inpcrd
>>>>
>>>> Needless, to say that I have tried several things to resolve this issue
>>>> among other things to manually entering the box dimensions into the
>>>> inpcrd, or to get via ptraj the inpcrd files for the various snapshots,
>>>> Non of which solved the problem.
>>>> I would like to ask whether it is possible to create a pbc box with out
>>>> solvating the system again ?.
>>>>
>>>> I thank you in advance for all your help.
>>>>
>>>> Arik
>>>>
>>>> _______________________________________________
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>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>
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>
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Received on Fri Aug 20 2010 - 15:00:05 PDT
