AMBER Archive (2004)

Subject: Re: AMBER: restart a MD after replacing molecules

From: cailliez (
Date: Thu Aug 26 2004 - 03:38:55 CDT

Thanks for your reply, Ross.

After few tests, I think I managed to do what I want.
First of all, I imaged the last restart file of my previous MD with
ptraj and outputted a pdb file.
I changed this PDB file, replacing the Ca2+ ion and the Cl- ions by
oxygen atoms from water molecules.
Finally, I changed a bit my leap script, adding the line setBox, so that
box informations
are written in the topology file. The script is now :
source leaprc_mod.ff99
mol = loadPdb snap.100mod.pdb
setBox mol centers
savepdb mol ecad12_CA12.pdb
saveAmberParm mol ecad12_CA12.crd
As I have an octahedron box, I have to change the variable IFBOX (1->2)
in the FLAG POINTERS section
and the FLAG BOX_DIMENSIONS section of the topology file (by putting the
box information taken from
my last restart file in the right format).
And I change also the crd file adding the last line of the last restart
file of my previous MD.

This seems to work when I use these files with sander, without giving me
error messages.
But I wonder if there were an easiest way to do it, for example using
ptraj, because manipulating lot
of files by hand can be a great source of errors.

If anyone see a problem in this protocole, I would appreciate to have
his/her opinion.
Sincerely yours,

Ross Walker a écrit:

>Dear Fabien,
>>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 ?
>Since you are not doing a restrt (no velocity info in the crd file) you have
>two options. One option would be to do as you say and cut and paste the box
>info - be very careful with the format. The other option, and something you
>might want to do anyway to remove any VDW clashes with your 3 added waters
>is to run a 100 steps of minimisation or so. If you just want to save
>yourself time equilibrating the water box then this will probably be fine.
>You will then get a rstrt file that has box info without having changed your
>structure too much. Simply removed the largest strains...
>I hope this helps
>|\oss Walker
>| Department of Molecular Biology TPC15 |
>| The Scripps Research Institute |
>| Tel:- +1 858 784 8889 | EMail:- |
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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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