[gmx-users] Re: Re: methanol simulation error

[Justin A. Lemkul]

mustafa bilsel wrote:
> Daer Justin,
> I changed the last line as
> MTH 660
> 
> I got the same error,
> Atomtype CMET not found
> 
> Do you mean this?
> 

I already explained to you what the problem was with that error:

http://lists.gromacs.org/pipermail/gmx-users/2011-January/057323.html

If you ignore the advice you've been given, you're unlikely to continue to get 
help.  What's more, you keep changing your information.  First, you were using 
"SOL 291" and the error was that there was no such moleculetype, then it was 
"SOL 660" with an atomtype error, then a topology that we suspect has one or 
both of these errors.

If you want free help, here are two tips:

1. Apply what you've been told, and respond directly with whether it did or did 
not work, with relevant output or evidence of a problem.
2. Do not change information mid-stream unless that change was offered to you as 
a potential fix or based on something you discovered to be problematic.  In this 
case, state what you've changed and why.  Otherwise, these threads become a 
jumble of impossibly disjointed information, which does not inspire anyone to 
jump in and help (or continue doing so).

-Justin

> best wishes
> mustafa
> 
> 
> 
> 
> Message: 1
> Date: Fri, 07 Jan 2011 07:04:05 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> Subject: Re: [gmx-users] Re: methanol simulation error
> To: Discussion list for GROMACS users <gmx-users at gromacs.org 
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <4D270135.5000703 at vt.edu <mailto:4D270135.5000703 at vt.edu>>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> 
> 
> mustafa bilsel wrote:
> 
> <snip>
> 
>  > ; Include Position restraint file
>  > #ifdef POSRES
>  > #include "posre.itp"
>  > #endif
>  >
>  > ; Include water topology
>  > #include "gromos43a1.ff/methanol.itp"
>  >
> 
> This topology defines the [moleculetype] name as "Methanol," which is 
> the name
> that needs to be used in the [molecules] directive below.  But then, 
> too, you're
> not using the same residue name either (MTH instead of MeOH), so it is 
> still not
> possible to say what's going wrong.
> 
> -Justin
> 
>  > [ system ]
>  > ; Name
>  > Protein in methanol
>  >
>  > [ molecules ]
>  > ; Compound        #mols
>  > Protein             1
>  > MTH               660
>  >
> 
> --
> ==============================
> ==========
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 

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

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

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