Hi Thomas,
I think I can manage the rest.
Thank you so much for your help.
Cheers,
Wook
On 07/23/2012 03:00 PM, steinbrt.rci.rutgers.edu wrote:
> Hi,
>
>> 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?
> it looks like CYS and CYX have minimally different internal coordinates in
> leap. This is a detail that would only matter when building systems for
> TI. I spontaneously have no good idea instead of switching the coordinates
> manually in your rst-files...
>
> Thomas
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
> _______________________________________________
> 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 Mon Jul 23 2012 - 06:30:03 PDT
