priyanka srivastava wrote:
Dear Justin,
Thanks a lot for replying back.
These are the two things that I have tried but still the peptide does
not come at the center:
1. trjconv -f complete_production.xtc -s test.tpr -o test.pdb -center
zero -b 22000
The "-center zero" flag is not an option in 3.3.3, are you sure these are the
commands you gave, and you are using the version you think you are?
I'm thinking that there is too big of a difference from 0 to 22 ns to allow
trjconv accurately apply the fix.
Try this:
trjconv -f complete_production.xtc -s test.tpr -center
As a basic test, it should re-center your chosen group (Protein) every frame,
allowing an iterative fix of the motion.
Select group for centering
Protein
Select group for output
System
2. trjconv -f complete_production.xtc -s test.tpr -center zero -fit
translation -b 22000 -o check2.pdb
Select group for translational fit
Same comments as a above, if you don't process every frame (or at least a
reasonably spaced subset), the algorithm doesn't tend to give the desired
output, or so I have noticed with -center and -pbc options.
-Justin
Selected 0: 'System'
Select group for centering
Selected 1: 'Protein'
Select group for output
System
I am using 3.3.3.
thnx,
Priyanka..
----- Original Message ----
From: Justin A. Lemkul <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users <[email protected]>
Sent: Tuesday, 12 August, 2008 12:05:26 AM
Subject: Re: [gmx-users] translation
priyanka srivastava wrote:
> Dear All,
>
> I really apologize for asking a peptide translation related question
> again. I have a lipid-peptide system and I have already carried out the
> production run for 20ns. The peptide has moved towards one of the edges
> (I didnt specify comm-grps in the mdp file). I have to translate the
> peptide in the center of the bilayer. While using trjconv it translates
> the peptide at 0,0,0 but shifts the lipid and water molecules as well
> such that eventually the peptide lies near the edge only!
Without seeing what command you've actually tried, it's hard to make any
recommendation.
> Is there any other tool which I should be using?
trjconv is the tool you want, it's just a matter of finding the right
options.
Under GMX 3.3.3, there is a -center flag that allows you to select a
group for
centering. In my protein/membrane systems, it has always worked well
(choose
Protein for the group to be centered).
-Justin
> Kindly suggest me something,
> Priyanka.
>
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========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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