From chemistry-request[ AT ]ccl.net Wed May 11 15:27:56 2005
Received: from proxy2.uh.cu (smtp2.uh.cu [200.55.139.213])
	by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4BJRpUD015641
	for <chemistry ## ccl.net>; Wed, 11 May 2005 15:27:53 -0400
Received: from localhost (localhost.localdomain [127.0.0.1])
	by proxy2.uh.cu (Postfix) with ESMTP
	id 648302FD4D; Wed, 11 May 2005 14:26:55 -0400 (CDT)
Received: from fq.uh.cu (unknown [192.168.3.4])
	by proxy2.uh.cu (Postfix) with ESMTP
	id 337642FD48; Wed, 11 May 2005 14:26:55 -0400 (CDT)
Received: from fq.uh.cu (IDENT:1565 #at# localhost [127.0.0.1])
	by fq.uh.cu (8.12.4/8.12.4/JP) with ESMTP id j4BEJhJZ024432;
	Wed, 11 May 2005 10:19:43 -0400
Received: from localhost (david;at;localhost)
	by fq.uh.cu (8.12.4/8.12.4/Submit) with ESMTP id j4BEJgIU024429;
	Wed, 11 May 2005 10:19:42 -0400
Date: Wed, 11 May 2005 10:19:42 -0400 (CDT)
From: David Santos Carballal <david ## fq.uh.cu>
To: lhhu ## yangtze.hku.hk
Cc: chemistry ## ccl.net
Subject: Re: CCL:Tinker input file
In-Reply-To: <Pine.LNX.4.61.0505111608210.26587 ## yangtze.hku.hk>
Message-ID: <Pine.LNX.4.44.0505111005450.23849-100000 ## fq.uh.cu>
MIME-Version: 1.0
Content-Type: TEXT/PLAIN; charset=US-ASCII
X-Virus-Scanned: by AMaViS snapshot-20020300
X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO 
	autolearn=failed version=3.0.3
X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net

Dear Holly:
If you want to generate the xyz file for TINKER to calculate a molecular
dynamics:
*first, you must create the molecule in hyperchem, gaussview, etc..., then
save it as protein data bank (*.pdb or *.ent).
*second you must run pdbxyz.exe included in the TINKER package via MS-DOS,
write the name of the file saved in the format *.pdb or *.ent and it will
create the file *.xyz
*third you must open the *.xyz with a word processing and assign manually
the force field atom type in the sixth column (after the cartesian
coordinates and before the connectivities), the place of the force
field atom type is filled with zeros by pdbxyz.exe.

David Santos Carballal

On Wed, 11 May 2005 lhhu ## yangtze.hku.hk wrote:

>
> Dear all CCLers,
>
> I would like to use free TINKER to calculated molecular dynamics. But the
> input file of tinker seems difficult to generate because the int or xyz
> file need to be assigned force field atom type first. Can anyone tell me
> about the most convenient way to generate the input xyz or int file? Is
> there any free program I can use?
>
> Thank you very much,
>
> Holly