[gmx-users] Re: Fatal error: Atomtype CB not found

[Justin A. Lemkul]

ITHAYARAJA wrote:
> Thank you for your informative reply, Sir,
> 
> Now I understood the problem but when i was tried with another ligand 
> (GSSG) It could be simulated. Later I found error for different ligand.
> 

So some systems work and others don't.  You haven't described what you're doing, 
or how you came up with these mixed force fields (which shouldn't be used).

> please give me the solution, what sort of force field should be applied?
> 

One that properly describes all components of your system in a self-consistent 
manner.  I have no idea what that might be, nor does anyone else on this list. 
A few hours of time in the literature will save you weeks, months, or years of 
wasted data collection using an inappropriate force field, especially one that 
is some hybrid of parameter sets.

-Justin

> 
> 
> 
> On 9 May 2011 21:27, ITHAYARAJA <ithayaraja at gmail.com 
> <mailto:ithayaraja at gmail.com>> wrote:
> 
>     Dear Sir
> 
>     Greetings!
> 
>     I am following every gromacs applications based on your manuals. I
>     now get stuck in grompp -energy minimization step during generation
>     of .tpr file for my ligand and protein. the error which i found is
>     the following,
> 
> 
>     Ignoring obsolete mdp entry 'title'
>     Ignoring obsolete mdp entry 'cpp'
> 
>     Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#
> 
>     WARNING 1 [file em.mdp, line unknown]:
>       Unknown or double left-hand 'coulomtype' in parameter file
> 
> 
>     checking input for internal consistency...
>     processing topology...
>     Opening library file /usr/share/gromacs/top/
>     ffG43a1.itp
>     Opening library file /usr/share/gromacs/top/ffG43a1nb.itp
>     Opening library file /usr/share/gromacs/top/ffG43a1bon.itp
>     Opening library file /usr/share/gromacs/top/ff_dum.itp
>     Generated 279 of the 1225 non-bonded parameter combinations
> 
>     -------------------------------------------------------
>     Program grompp, VERSION 4.0.7
>     Source code file: ../../../../src/kernel/toppush.c, line: 947
> 
>     Fatal error:
>     Atomtype CB not found
>     -------------------------------------------------------
> 
>     Sir, I couldn't understand what did it refers to? So I kindly
>     request you spare your little time from your busy schedule to solve
>     this problem.
> 
>     Thank you, Sir
> 
> 
>     -- 
>     **
>     Ithayaraja M,
>     Research Scholar,
>     Department of Bionformatics,
>     Bharathiar University,
>     Coimbatore 641 046,
>     Tamil Nadu
>     India
> 
> 
> 
> 
> -- 
> **
> Ithayaraja M,
> Research Scholar,
> Department of Bionformatics,
> Bharathiar University,
> Coimbatore 641 046,
> Tamil Nadu
> India
> 

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

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

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