-
Hello Sir ,
I am a graduate student in chemistry department at Mississippi State
University. I am trying to calculate the binding energiers of the receptor
MMB4 in explicit method using thermodynamic integration. I have
successfully made zero charges on the receptor atoms and now i am trying
remove the vanderwaals forces. Due to the long simulations, some of the
water molecules have gone too far in the periodic box, as a result in the
.rst file i am getting * symbols for the coordinated instead of numbers i.e
************** instead of 123.222(something like that). I looked at the
amber 8 manual, to added iwrap=1, to input file so that it reimages
molecules and keep them with in the periodic box, before it writes to the
output and rst files. But after using this also I got *** in my .rst file.
Due to which I cannot give the .rst file of this simulation for the next
one. I have even tired to create reimaged rst file using ptraj but it is not
working properly. Is there any solution for this. Please tell me. If you
need additional information, let me know about it.
Thanking you in advance
Manikanthan
--
Manikanthan Bhavaraju
Graduate Teaching Assistant
Dept. of Chemistry
Mississippi State University
office no : 662-325-4633
MS -39762
USA.
--
--
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 09 2010 - 09:00:07 PDT
