[gmx-users] error with grompp

[Shima Arasteh]

So just entering the -pname NA and -nname CL !

 
Sincerely,
Shima


----- Original Message -----
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Friday, June 29, 2012 5:36 PM
Subject: Re: [gmx-users] error with grompp



On 6/29/12 8:54 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> 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.
>

Well, it is a correct outcome of genion, but it is incorrect usage.  From genion -h:

"The ion molecule type, residue and atom names in all force fields are the
capitalized element names without sign. This molecule name should be given
with -pname or -nname, and the [molecules] section of your topology updated
accordingly, either by hand or with -p. Do not use an atom name instead!"

-Justin

> 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
>
>

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

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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