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.top ecad12_CA12.crd
quit
********
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,
Fabien
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
>Ross
>
>/\
>\/
>|\oss Walker
>
>| Department of Molecular Biology TPC15 |
>| The Scripps Research Institute |
>| Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
>| http://www.rosswalker.co.uk/ | PGP Key available on request |
>
>
>
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--
__________________________________________________________________
Fabien Cailliez Tel : 01 58 41 51 63
Laboratoire de Biochimie Théorique e-mail : cailliez.ibpc.fr
IBPC 13, rue Pierre et Marie Curie
75005 Paris
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Received on Thu Sep 02 2004 - 01:15:11 PDT
