AMBER Archive (2004)

Subject: AMBER: restart a MD after replacing molecules

From: cailliez (
Date: Wed Aug 25 2004 - 09:03:41 CDT

Dear all,

I am running MD on a system containing a protein and three calcium ions
linked to this
protein with explicit water molecules.
I have already a stable MD of this system and I would like to delete one
calcium ion from
this system to see what happens. I want to use as a starting
configuration the last configuration
of my system with three calcium, so that my water box would be almost
I tried to do that manually, replacing one Ca2+ and two Cl- by three
water molecules
in a pdb file I obtained after imaging the last restart file of my
previous MD, and ran leap with this
script :
source leaprc_mod.ff99
mol = loadPdb snap.100mod.pdb
savepdb mol prot_CA12.pdb
saveAmberParm mol prot_CA12.crd
But when I tried to run an MD with the prot_CA12.crd file as input, it
turned out that my system
do not have any box size.
I think I can just take the last line of the last restart file of my
previous MD and put it at the end
of the crd file but I am not sure this is correct to do this.

Is this the correct way to do what I want ? Or is there any better way
to do it ?

Thanks in advance,

Fabien Cailliez				Tel : 01 58 41 51 63				
Laboratoire de Biochimie Théorique	e-mail :
IBPC	13, rue Pierre et Marie Curie 		
75005 Paris					

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