# Re: jarrod

From: Matheus Froeyen <Matheus.Froeyen.rega.kuleuven.ac.be>
Date: Fri, 13 Jun 2003 09:36:14 +0200

Hi,

you could use the open source DMS software from

http://www.cgl.ucsf.edu/Overview/software.html

At the end of this mail I include an example unix script which
calls the DMS software and which can easily be modified.

First snapshots are saved as pdb files
and then preprocessed to be compatible with DMS.
Then DMS is run and the output is analyzed
(simple averaging over the trajectory,
binning into categories: chains and polar, nonpolar atoms, ...).

best regards
mathy froeyen

-------------------------------------------------------------

#!/bin/csh -f
#Run.sas_analysis

/bin/rm -f sas.tbl
/bin/rm -f dms.inf
touch dms.inf

cat << eof > nawk1.in
{
if (\\$3 !~ /^H/) print \\$0
}
eof
cat << eof > nawk2.in
BEGIN {total=0; rnaB=0; rnaS=0; rnaP=0; hnaB=0; hnaS=0; hnaP=0; rnaBP=0;
rnaBNP=0; rnaSP=0; rnaSNP=0; hnaBP=0; hnaBNP=0; hnaSP=0; hnaSNP=0; oh=0}

{
if (NF > 7) {
( total += \\$8 )
if (\\$1 ~ /^P/) { hnaP += \\$8 }
if (\\$1 ~ /^A/) {
if (\\$3 ~ /'/) {
(hnaS+= \\$8)
if (\\$3 ~ /^O/) {hnaSP += \\$8}
if (\\$3 ~ /^O2/) {oh += \\$8}
if (\\$3 ~ /^N/) {hnaSP += \\$8}
if (\\$3 ~ /^C/) {hnaSNP += \\$8}
}
if (\\$3 !~ /'/) {
(hnaB+= \\$8)
if (\\$3 ~ /^O/) {hnaBP += \\$8}
if (\\$3 ~ /^N/) {hnaBP += \\$8}
if (\\$3 ~ /^C/) {hnaBNP += \\$8}
}
}
if (\\$1 ~ /^R/) {
if (\\$3 ~ /P/) {rnaP += \\$8}
if (\\$3 !~ /P/) {
if (\\$3 ~ /'/) {
(rnaS += \\$8)
if (\\$3 ~ /^O/) {rnaSP += \\$8}
if (\\$3 ~ /^N/) {rnaSP += \\$8}
if (\\$3 ~ /^C/) {rnaSNP += \\$8}
}
if (\\$3 !~ /'/) {
(rnaB += \\$8)
if (\\$3 ~ /^O/) {rnaBP += \\$8}
if (\\$3 ~ /^N/) {rnaBP += \\$8}
if (\\$3 ~ /^C/) {rnaBNP += \\$8}
}
}
}
}
}
END {print rnaB, rnaBP, rnaBNP, rnaS, rnaSP, rnaSNP, rnaP, hnaB, hnaBP,
hnaBNP, hnaS, hnaSP, hnaSNP, hnaP, total, oh}
eof

set i = 1
while (\$i < 11)
cat << eof > carnal.in
FILES_IN
PARM p1 /d3/nucl/md/ara/parm.top;
STREAM s1 /d3/nucl/md/ara/md_\$i.center.cor.Z;
FILES_OUT
COORD c1 pdb PDB;
DECLARE

OUTPUT
COORD c1 s1 ATOM 541;
END
eof
carnal < carnal.in
set j = 1
while (\$j < 501)
nawk -f nawk1.in pdb.\$j > p.\$j
dms p.\$j -a -o dms.out >>& dms.inf
nawk -f nawk2.in dms.out >> sas.tbl
mv dms.out dms.out.old
# mv dms.out dms.out.\$j
# gzip dms.out.\$j
/bin/rm -f p.\$j
. j++
end
/bin/rm -f pdb.*
. i++
end

-----------------------------------------------------------
Jarrod Wesley Barnes wrote:

> I was curious to know if one could calculate the solvent
> acessible surface area for an atom or residue in a trajectory
> file over the course of a MD simulation in one of the programs
> associated with Amber. If not, is there a program that is
> capable of doing this calculation over the course of the
> trajectory ?
>
> thanks,
> Jarrod Barnes
> Grad Student at UGA BIOCHEM
> PI: Dr. Rob Woods
Received on Fri Jun 13 2003 - 08:53:01 PDT
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