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If you just need what you said, This is it.

$ awk '{$2+=5294;$6-=126;print}' OFS="\t" file
ATOM 5295 OW SOL X 131 77.820 57.470 97.740 1.00 0.00
ATOM 5296 ...

Give us an example of the current data and expected changes...we shall try

Try:awk 'NR==FNR{a[$0]=1;next}a[FNR]==1{gsub ("H","Na+")}1' test testsds.pdb

Try:awk '{for (i=1;i<=NF;i++) $i=sprintf ("%.2f",$i)}1' file

You can make an x keyboard to anything, but I have been spared that education. I have some bits that make my pc numeric keypad work, but every time I sneeze, it flips back! Maybe a function key, or...

Only print unique field 6
awk '!x[$6]++ {print $6}' file

print complete line
awk '!x[$6]++' file

... | sort | uniq | while read var; do
do something with $var here
done

Try: awk '{print substr($0,25,2)}' file | sort | uniq

Well, it's octal 0174, so:echo x|tr 'x' '\174'

echo '\0174'
|

By shell:

cat template

#!/bin/bash -l

#$ -S /bin/bash
#$ -l h_rt=1:00:0
#$ -l mem=4G
#$ -N XXX
#$ -pe qlc 24
#$ -P XXX
#$ -wd /home/uccaxxx/Scratch/222PdT/3vac/c0001/

mpirun -m...

just for reference:

BEGIN{OFS="\t"; ARGV[ARGC++] = ARGV[1] }
function abs(i) {return (i<0)?-i:i}

FNR==NR{
for(i=1;i<=NF;i++)
if ($i<0) {
m=($i<m)?$i:m
nC[i]
}
next...

Do you want to determine the largest negative among ALL the columns and add its absolute value to ALL the negative values for ALL the columns?
Or you want to determine the largest negative PER...

ALL the columns? Even the ones that say HETATM, C, and UNK?

You'd better just tell us which columns.

Or better yet: An example of your input and output data!!

---------- Post updated at...

ok, try this:

BEGIN{OFS="\t"; ARGV[ARGC++] = ARGV[1] }
function abs(i) {return (i<0)?-i:i}

FNR==NR{
for(i=1;i<=NF;i++)
if ($i<0)
m[i]=($i<m[i])?$i:m[i]
next
}
{
...

You're doing better than usual, it sometimes takes 4 pleas for a poster to show their data, let alone admit what they want :)

Working on it...

---------- Post updated at 11:29 AM ----------...