[gmx-users] merger ligand and protein to constriant

[Fan, Fenghui]

Try the following way:



But you shoul get you top file and gro file without the ligand. Then If your protein has 100 residues, add you ligand as residue 101 in the gro file. After residue add the "TER" . In ddition, adding the ligand ITP file to the later part of the Gro file. 


-----Original Message-----
From: gmx-users-bounces at gromacs.org on behalf of ??
Sent: Tue 9/12/2006 7:07 AM
To: gmx-users at gromacs.org
Subject: Re:[gmx-users] merger ligand and protein to constriant
 
What about merging  the ligand the the protein by DeepView? 


In your mail:
>From: "kanin wichapong" <kwichapong at gmail.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] merger ligand and protein to constriant
>Date:Tue, 12 Sep 2006 13:40:59 +0200
>
>Hi all
>  I already look in the turorial however that is not the thing that I try to
>look for. I would like to merge the ligand into the protein and then make
>the contrain between two atoms, one from the liagand and one from the
>protein. However, as far as I know, I can do the constraint or restraint
>just in the one chain. I cant do that with the different chain. So that i
>try to merge ligand chain and protein chain. I tried to do that with pdb2gmx
>but it is not work. So that i would like to know is there any way to merge
>the ligand chain with the protein chain.
>    Thanks for all your suggstions
>
>Best Regard
>Kanin
>_______________________________________________
>gmx-users mailing list    gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>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


_______________________________________________
gmx-users mailing list    gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
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