[gmx-users] AMBER and gromacs atoms renaming

Shay Amram shayamra at post.tau.ac.il
Sun Aug 10 18:40:58 CEST 2008

Can this help?
I found using the users-gmx mailing list archives (you should search the
archive before posting):

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
gmx-users mailing list    gmx-users at gromacs.org
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

More information about the gromacs.org_gmx-users mailing list