[gmx-users] Need help!!!

[Justin A. Lemkul]

#ZHAO LINA# wrote:
> 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.
> 

Indeed.  But I'm also a fan of solving one problem at a time.  A broken force 
field file won't get fixed by trying to simultaneously accommodate a new 
organization and understand the intrinsics of Gromacs.

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

Glad it was useful.  When you say "nearly," were there parts that didn't make 
sense/didn't work?

> Thanks with best regards,
> 
> lina
> 
> P.S actually you can upgrade your website also. ^_^ 

I realize that.  But I do not have the time to do it, nor will I anytime in the 
near future.  I've got a system that works, and if users are comfortable enough 
with the tutorial as is, then (as you say) it should be easy to convert over to 
the new system.  For anyone new to the game, it may be useful to do the tutorial 
as is, learn Gromacs a bit more thoroughly, then undertake an adventure :)

-Justin

> ________________________________________
> 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.
> 
> -Justin
> 
>> ------------------------------------------------------------------------
>> *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
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> 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
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================