I just found one more thing.
In the case of CYM (deprotonated cysteine), HB3 appears earlier than HB2
while it's the other way around in the case of CYS.
Therefore, the order of the atoms becomes different between two crd files.
On 07/23/2012 02:30 PM, Wook Lee wrote:
> Hi, Thomas
>
> Thank you for your answer.
>
> You are right.
> I found the difference between two crd files,
> but I still don't know why leap assigns coordinates in this way.
> I generated two crd files from two pdb files which are different from
> each other only in disappearing atom.
> However, when leap generates crd files from those pdb files, it
> exchanges the coordinates for HB2 and HB3 of cysteine residue.
> So HB2 atom of first crd file has the coordinate of HB3 atom of second
> crd file and vice versa.
>
> Do you know how I can fix this problem?
>
> Cheers,
> Wook
>
>
>
>
>
> I generated prmtop and crd file from same
>
>
> On 07/21/2012 07:16 PM, steinbrt.rci.rutgers.edu wrote:
>> Hi,
>>
>>> WARNING: Local coordinate 34 differs from partner coordinate
>>> 34 !
>>> SANDER BOMB in subroutine sc_check_and_adjust
>>> Atom coordinate disagreement
>>> Check input files.
>>>
>>> I know that this error occurs when the coordinates of two crd files are
>>> different significantly,
>>> but I checked several times and am quite sure that there is no
>>> difference between two crd files except the coordinate of disappearing
>>> atom.
>> It is quite unlikely that the code calculates the difference wrong. Make
>> sure you checked the actual files you feed to sander. Coordinate 34 (i.e.
>> the x-coordinate of the 12th) atom is different.
>>
>> Thomas
>>
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Received on Mon Jul 23 2012 - 06:30:03 PDT
