VMD-L Mailing List

From: koushik.k (koushik.k_at_students.iiit.ac.in)
Date: Tue Aug 03 2010 - 06:45:25 CDT

hi VMD users,

My system is protein + water sphere (not water box).
I have done SMD using constant velocity pulling.
I want to save the coordinates for all frames.

I have tried catdcd, and also the SAVE COORDINATES option in the VMD main
window.
But, i have been getting a PDB WRITE ERROR.

when i went through the VMD mailinglist, i have found that the error may
be due to unexpected values of X,Y,Z or Beta or Occupancy.

So, i tried fitframes.tcl script to fix the system's transformation and
rotation.Even that did not help.
Then i tried to fix the center of mass of system to the center coordinates
{0 0 0}. But, still i was getting a PDB WRITE ERROR.

The PDB WRITE ERROR was always for an atom belonging to a water molecule.

Upon close inspection, i found out that when you load the psf and dcd file
in VMD and view the system through the trajectory, you find that some
water molecules shoot out from the water sphere.

This might be the reason for getting a PDB WRITE ERROR because when the
water molecules shoot out their X,Y,Z values become too high for VMD to
write.

Can anyone suggest a solution to this problem.

Regards,
Koushik.K 

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