AMBER Archive (2004)

Subject: Re: AMBER: file corruption with ptraj

From: cailliez (Fabien.Cailliez_at_ibpc.fr)
Date: Mon Oct 18 2004 - 10:32:32 CDT

Hi Steve,

The problem is that when you strip water molecules, your topology
file is not good anymore to analyse file1_2.mdcrd.
To analyse this file, you have to create a topology file which does not
contain
any water (you can make it easily with Leap), but you will certainly have
a problem of box.
If you only want to look at the RMSD and atomic fluctuations,
I think you should use only one script like this one :
trajin file1.mdcrd
trajin file2.mdcrd
strip :WAT
rms first mass out rms.dat time 5 @CA,C,N
atomicfluct out rmsf.dat :1-398 byres
go

This should work.
If you want to use the trajectory file (to look with VMD for example), I
suggest you do :
trajin file1.mdcrd
trajin file2.mdcrd
strip :WAT
rms first mass out rms.dat time 1 @CA,C,N
trajout nowat.trj nobox
go

(the line "rms first mass out rms.dat time 1 @CA,C,N" is just here to
remove overall
translation and rotation movements but is not necessary)
and with leap, create a topology file without water molecules to use
with nowat.trj

I hope this will help you,
Fabien 

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

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