[gmx-users] convert B-factor

[Tsjerk Wassenaar]

Hi Antonio,

You can do something like:

grep -v "^#@" rmsf1.xvg > rmsf1.dat
grep -v "^#@" rmsf2.xvg > rmsf2.dat
paste rmsf1.dat rmsf2.dat | awk '{print $4-$2}' > difference.dat

That will give you a file with the rmsf difference. You can use
editconf to read such data into the b-factor field, although you may
need to modify the file a bit. Check editconf -h for that.

Hope it helps,

Tsjerk



On Mon, Dec 28, 2009 at 7:52 AM, AntonioLeung <royaltramp at live.cn> wrote:
> I know how to calculate, and have calculated the RMSF of  two trajectories
> (of the same molecule), and I want to compare the two RMSFs. I want convert
> their
>
> discrepancy into B-factors. Can you tell me more detailed?
>
>
>
> ------------------ Original ------------------
> From:  "Mark Abraham"<Mark.Abraham at anu.edu.au>;
> Date:  Mon, Dec 28, 2009 11:04 AM
> To:  "Discussion list for GROMACS users"<gmx-users at gromacs.org>;
> Subject:  Re: [gmx-users] convert B-factor
>
> AntonioLeung wrote:
>> Dear all,
>> I want to convert the difference of two rmsf data sets into B-factor of
>> a coordinate (to illustrate their difference by coloring the structure
>> by B-factor), can anyone tell me how to do it?
>
> g_rmsf -h
>
> Mark
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist