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

[ITHAYARAJA]

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.

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




On 9 May 2011 21:27, ITHAYARAJA <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
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