This is what I mean by "quick and dirty".
#!/bin/bash
# Reads the output of "g_sas" per residue (-or) and writes only the residues
you want.
# Diego E.B. Gomes, Roberto D. Lins, Pedro G. Pascutti, Thereza A. Soares
# mailto: [email protected]
#1 ) To perform multiple g_sas (will write out all residues in many files)
for ((frame=0;frame<=10;frame=frame+1)) do
g_sas_4 -s md.tpr -f md.xtc -n index.ndx -or resarea.${frame} -o area.${frame}
-oa atomarea.${frame} -b ${frame} -e ${frame} <<EOF
Protein
Protein << you can replace this by your FAVORITE residues (though you will
need to modify the rest of the script).
EOF
done
# 2) To processs the many many files and output the area for your desired
residues:
#list of residues to print, in sequential order.
list="1 2 3 5 8 13 34"
echo "# resarea for residues $list" > resarea.favorites.dat
for ((frame=0;frame<=1000;frame=frame+1)) do
echo -ne "$frame \r"
cat resarea.${frame}.xvg |grep -v "#" |grep -v "@" > tmp
i=1
while read a b c ; do # reads the text file
residue[$i]=$a
sas[$i]=$b
stdev[$i]=$c
i=$(($i+1))
done < "tmp"
j=1
for i in `echo $list` ; do
out[$j]=${sas[$i]}
j=$(($i+1))
done
echo $frame ${out[@]} >> resarea.favorites.dat
done
done
# :)
On Jul 7, 2011, at 9:17 PM, Justin A. Lemkul wrote:
>
>
> ahmet yıldırım wrote:
>> There are hydrophilic and hydrophobic SASA values versus simulation time in
>> the output file (area.xvg). I want to hydrophilic and hydrophobic SASA
>> values versus residue.
>
> That's not implemented, but it would probably be rather easy to modify the
> code to do so.
>
> -Justin
>
>> 2011/7/7 Justin A. Lemkul <[email protected] <mailto:[email protected]>>
>> ahmet yıldırım wrote:
>> Dear users,
>> I want to calculate hydrophilic and hyrophobic SASA value of
>> each residue in protein. I used a command as the following:
>> g_sas -f run.xtc -s run.tpr -or protein_protein.xvg
>> Select a group for calculation of surface and a group for output
>> select a group: 1 (protein)
>> select a group: 2 (protein)
>> But there is SASA value of each residue in the output file. How
>> can I seperate the residues as a hydrophilic and hyrophobic SASA?
>> This is already in the output file. Check the legends of area.xvg
>> and you will see.
>> -Justin
>> -- ==============================__==========
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>> http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> ==============================__==========
>> -- gmx-users mailing list [email protected]
>> <mailto:[email protected]>
>> http://lists.gromacs.org/__mailman/listinfo/gmx-users
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>> --
>> Ahmet YILDIRIM
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list [email protected]
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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--
Diego E. B. Gomes
Instituto de Biofísica Carlos Chagas Filho
Universidade Federal do Rio de Janeiro
Brasil +55 21 2562.6507
/temp @ Laboratoire de Biologie et de Pharmacologie Appliquée
Ecole Normale Supérieure, Cachan, France
France +33 07 8638.8099
--
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