Dear all,
Currently I am using amber8 to calculate the binding energies using TI.
During the first step while making the atomic charges zero using TI, for
the substrate molecule (explicit solvent model) at clambda=0.70292, I ran
the simulations for 19 ns. At the 19th ns the rst file corrupted as a result
I am unable to submit the previous .rst file for next simulation. On
visualization in VMD I have observed some of the hydrogen molecules has
diffused some what out of the box. I have reimaged them back into the box
using ptraj, but this gives only reimaged residues with new coordinates.
But I am trying to reimage all the residues with new velocities using ptraj
and I have used the following script.
trajin sub.rst
trajout sub_reimage.rst restart
center :1-1
image center familiar
go
1 is the substrate molecule. But the new .rst file generated by ptraj has
coordinated but has 0.0000 for the velocities. How can I get new velocities
using ptraj. Any help is really appreciated.
I have also tired iwrap=1, but it didn't work.
manikanthan
--
Manikanthan Bhavaraju
Graduate Teaching Assistant
Dept. of Chemistry
Mississippi State University
office no : 662-325-4633
MS -39762
USA.
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Received on Wed Aug 18 2010 - 23:30:07 PDT
