[gmx-users] AMBER and gromacs atoms renaming

[Tsjerk Wassenaar]

Hi,

Well, sed's a good friend to have in these cases :)

e.g. converting lysine residue names:
sed -e 's/LYSH/LYP /' -e 's/LYS/LYN/' gromacs.pdb > amber.pdb

or converting the C7 of thymine to C5M:
sed -e 's/\(^.\{13\}C\)7  THY/\15M THY/' gromacs.pdb > amber.pdb

Note that this can be easily extended to give you a complete dictionary.
But with the other options given.., it's a matter of taste.

Cheers,

Tsjerk

On Sun, Aug 10, 2008 at 6:40 PM, Shay Amram <shayamra at post.tau.ac.il> wrote:
> Can this help?
> http://www.gromacs.org/pipermail/gmx-users/2006-March/020599.html
> I found using the users-gmx mailing list archives (you should search the
> archive before posting):
> http://www.gromacs.org/component/option,com_wrapper/Itemid,165/
>
> If that doesn't solve your problem, you can always write some short PERL
> script to do
> the renaming for you.
>
> Good Luck,
> -Shay Amram
>
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Ragnarok sdf
> Sent: Sunday, August 10, 2008 19:05 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] AMBER and gromacs atoms renaming
>
> Hi, I am running a simulation of a protein DNA complex, and for this i
> am using AMBER99 forcefield. The problem is that every complex I need
> to run, I have to rename several residues and atoms, especially
> hydrogen atoms one by one (well, actually using replace tool). And
> this takes hours to get done.
> Is there any shortcut I can use, like a software that prepares my pdb
> files for an AMBER run, or something close to that?
> If not, Ill just keep doing things by hand.
> Thank you
> Fabrício Bracht
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623