[gmx-users]

[rob yang]

I think that might've been a typo in the tutorial, but don't quote me on 
this.  The -c should be enough to supply grompp with the necessary initial 
structure info.
As for additional tutorials on make_hole, I havn't found anything yet. I 
found the combination of Dr. Faraldo-gomez, Smith, et al's paper Eur Biophys 
J (2002) 31: 217-227 and the tutorial helped alot. I know that the 
gromacs-related details can be a lil frustrating and confusing which is why 
we are here.

rob

>From: Weidong Xin <xin at sun3.oulu.fi>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: Re: [gmx-users] Date: Thu, 11 Aug 2005 10:08:16 +0300 (EEST)
>MIME-Version: 1.0
>Received: from elvira.ekonomikum.uu.se ([130.238.164.5]) by 
>mc7-f22.hotmail.com with Microsoft SMTPSVC(6.0.3790.211); Thu, 11 Aug 2005 
>00:16:03 -0700
>Received: by elvira.ekonomikum.uu.se (Postfix, from userid 204)id 6A14B2D6; 
>Thu, 11 Aug 2005 09:16:01 +0200 (MSZ)
>Received: from elvira.ekonomikum.uu.se(127.0.0.1) by 
>elvira.ekonomikum.uu.se via virus-scan id s26692; Thu, 11 Aug 05 09:15:56 
>+0200
>Received: from xray.bmc.uu.se (xray.bmc.uu.se [130.238.41.195])by 
>elvira.ekonomikum.uu.se (Postfix) with ESMTP id 05D82207;Thu, 11 Aug 2005 
>09:15:54 +0200 (MSZ)
>Received: from xray.bmc.uu.se (localhost.localdomain [127.0.0.1])by 
>xray.bmc.uu.se (Postfix) with ESMTPid EC48225080; Thu, 11 Aug 2005 09:15:53 
>+0200 (CEST)
>Received: from colibri.its.uu.se (colibri.its.uu.se [130.238.4.154])by 
>xray.bmc.uu.se (Postfix) with ESMTP id 6206824BDCfor 
><gmx-users at gromacs.org>; Thu, 11 Aug 2005 09:15:51 +0200 (CEST)
>Received: by colibri.its.uu.se (Postfix, from userid 211)id 51335110; Thu, 
>11 Aug 2005 09:15:51 +0200 (DFT)
>Received: from colibri.its.uu.se(127.0.0.1) by colibri.its.uu.se 
>viavirus-scan id s14345; Thu, 11 Aug 05 09:15:47 +0200
>Received: from oulu.fi (ousrvr.oulu.fi [130.231.240.1])by colibri.its.uu.se 
>(Postfix) with ESMTP id 37C4A110for <gmx-users at gromacs.org>; Thu, 11 Aug 
>2005 09:15:47 +0200 (DFT)
>Received: from cc.oulu.fi (sun3.oulu.fi [130.231.240.13])by oulu.fi 
>(8.13.1/8.13.1) with ESMTP id j7B78HwY009539for <gmx-users at gromacs.org>; 
>Thu, 11 Aug 2005 10:08:17 +0300 (EEST)
>Received: from sun3.oulu.fi (sun3.oulu.fi [130.231.240.13])by cc.oulu.fi 
>(8.12.10/8.12.10) with ESMTP id j7B78Gtp004238for <gmx-users at gromacs.org>; 
>Thu, 11 Aug 2005 10:08:16 +0300 (EEST)
>X-Message-Info: sPHCaSLRLXy1l6Q9EyIkCGnSJwUfwoLGbP33GGUFNbQ=
>X-Original-To: gmx-users at gromacs.org
>Delivered-To: gmx-users at xray.bmc.uu.se
>X-X-Sender: xin at sun3.oulu.fi
>References: 
><mailman.289.1123670039.1474.gmx-users at gromacs.org><Pine.GSO.4.58.0508101533280.10684 at sun3.oulu.fi>
>X-BeenThere: gmx-users at gromacs.org
>X-Mailman-Version: 2.1.4
>Precedence: list
>List-Id: Discussion list for GROMACS users <gmx-users.gromacs.org>
>List-Unsubscribe: 
><http://www.gromacs.org/mailman/listinfo/gmx-users>,<mailto:gmx-users-request at gromacs.org?subject=unsubscribe>
>List-Archive: <http://www.gromacs.org/pipermail/gmx-users>
>List-Post: <mailto:gmx-users at gromacs.org>
>List-Help: <mailto:gmx-users-request at gromacs.org?subject=help>
>List-Subscribe: 
><http://www.gromacs.org/mailman/listinfo/gmx-users>,<mailto:gmx-users-request at gromacs.org?subject=subscribe>
>Errors-To: gmx-users-bounces at gromacs.org
>Return-Path: gmx-users-bounces at gromacs.org
>X-OriginalArrivalTime: 11 Aug 2005 07:16:03.0840 (UTC) 
>FILETIME=[88B42800:01C59E44]
>
>
>Dear gmx-users,
>
>Could you please tell me what is the mean of option s
>in file 'mdrun_make_hole.tar.gz' for instance 'grompp -f run.mdp -s
>insert.tpr -c outbilayer.pdb -r outbilayer.pdb -p ...'?
>If i want to run program 'mdrun_make_hole', where can i get a guide as a
>beginner in Gromacs except 'Putting Proteins into Bilayers (v 3.1)'?
>
>Thank you!
>Weidong
>_______________________________________________
>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.