[gmx-users] Need help!!!

#ZHAO LINA# ZHAO0139 at e.ntu.edu.sg
Thu Sep 2 15:30:01 CEST 2010

But it's a bit trivial to modify those things if you just following those steps by steps.
Using the latest version can save lots of works.

By the way, thanks for the website, I once followed that too (nearly step by step also).

Thanks with best regards,


P.S actually you can upgrade your website also. ^_^ 
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at vt.edu]
Sent: Thursday, September 02, 2010 9:12 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Need help!!!

#ZHAO LINA# wrote:
> Make sure your gromacs is the latest version.
> If not, update and try again.

The tutorial is specifically written for version 4.0.5, but will be compatible
with any version <4.5.  Since the re-organization of the force field
directories, the information provided in the tutorial is not correct.

I would recommend not upgrading until the OP has sorted out the problem and can
then (maybe) work out the appropriate translation to the version 4.5.x scheme.


> ------------------------------------------------------------------------
> *From:* gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on
> behalf of praba vathy [sumipraba2003 at gmail.com]
> *Sent:* Thursday, September 02, 2010 9:06 PM
> *To:* gmx-users at gromacs.org
> *Subject:* [gmx-users] Need help!!!
> Hi,
> I am using simulation for a membrane protein.
> So i have downloaded the dppc.pdb along with it's topology files.
> I have used the following steps for the simulation (Based on the link:
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/01_pdb2gmx.html).
> We have used the commands and steps as described in the above link.
> But we have got a fatal error (Atom type C not found) while running this
> command,
> grompp -f mini.mdp -c dppc128.gro -p topol_dppc.top -o em.tp <http://em.tp>
> I cant sort out this problem.
> Please anybody help me to sort out this problem.
> Awaiting for your valuable replies.
> Praba


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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