AMBER Archive (2006)

Subject: AMBER: Restarting with new topology

From: Sergey Samsonov (
Date: Thu Nov 23 2006 - 10:39:53 CST

Dear Ambers,

I was trying to run the simulation with the new topology file where I
introduced the perturbed type for the molecule of the interest in order
to make Free Energy Perturbation calculations. For this sake I made pdb
from the frame (this frame is related to the state of the system I'm
interesting in, in particular,
at this frame the water molecule is occupying the site of interest and
I'm trying to calculate the free energy of it) using trajout to create
restart file firstly and then ambpdb to create pdb file itself. I
modified the perturbed type of the water in xleap and saved the new
topology. Then I tried to deal with the problem
related to the absence of the periodic box in the new topology. I tried
to compare the old topology file and the new one and to combine them
somehow to introduce the information about the box. After all I didn't
succeed since either I had error like

''(NTB /= 0 && NTP /= 0) but IFBOX == 0 This combination is not supported"


"| Flags: MPI
 getting new box info from bottom of inpcrd
 peek_ewald_inpcrd: SHOULD NOT BE HERE"

or the system was blowing out. I tried some different possibilities.

Besides this problem I'm not sure if I really can get the velocities
from the created restart file. Or should I use irest=0?

I'll appreciate it very much if anyone could give me advice how to deal
with this problem.

Thank you in advance!


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to