[gmx-users] CHARMM36 force field available for GROMACS

[Mark Abraham]

Nice trick - I didn't realise you could chain and group sed regular
expressions that way!

Neither did I know pdb2gmx had an .arn database.

That's two things I've learned... Can I go home now? :-D

Mark
On Mar 10, 2014 7:32 AM, "Tsjerk Wassenaar" <tsjerkw at gmail.com> wrote:

> cat $pdbfile | sed 's/TIP3/SOL /' | sed 's/ OH2 SOL/ OW  SOL/' | sed 's/
> > H1  SOL/ HW1 SOL/' | sed 's/ H2  SOL/ HW2 SOL/' | sed 's/ SOD SOD/ NA  NA
> > /g
> > ' | sed 's/ CLA CLA/ CL  CL /g'
> >
>
> Something like this in one command?:
>
> sed 's/TIP3/SOL /;/SOL/{s/OH2/OW /;s/H1 /HW1/;s/H2 /HW2/;};s/SOD/NA
> /g;s/CLA/CL /g;' $pdbfile
>
> Cheers,
>
> Tsjerk
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
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