[gmx-users] error with grompp

[Justin A. Lemkul]

On 6/29/12 9:04 AM, Shima Arasteh wrote:
>
>
> Hi,
>
> Check out the order of sections which you have included in your .top file. I always got this error because of the wrong orders of sections.
>

Incorrect order will lead to a series of "non-matching atom names" in the grompp 
output.  In this case, the error comes from incorrect usage of genion (see my 
previous post).

-Justin

>
>
>
> Cheers,
> Shima
>
>
> ________________________________
> From: "reisingere at rostlab.informatik.tu-muenchen.de" <reisingere at rostlab.informatik.tu-muenchen.de>
> To: gmx-users at gromacs.org
> Sent: Friday, June 29, 2012 5:24 PM
> Subject: [gmx-users] error with grompp
>
> Hi everybody,
> I added ions to the solvent around my structure with the command:
>
> genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1
> -neutral -pname NA+ -nname CL-
>
> and then I select the 13 (SOL)
>
>
> Now I have in my topology file
>
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> DUM             30066
> SOL         14305
> NA+              32
> CL-              32
>
> which is correct in my opinion.
>
> But now when I want to run grompp:
>
> grompp -v -f minim_solv.mdp -c 3m71_minim_ion.gro -p 3m71.top -o
> 3m71_minim_ion.tpr 2>>logErr 1>>logOut
>
>
> I always get the error:
>
> No such moleculetype NA+
>
>
> although I already included the ion topology file:
>
> ; Include topology for ions
> #include "amber03.ff/ions.itp"
>
> What is wrong here?
>
> Best Eva
>
>

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

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