[gmx-users] Membrane protein tutorial

Pawan Kumar pawan.chinari at gmail.com
Thu Apr 9 06:51:28 CEST 2009

Hello Mark Sir,

I have tried that way also.
The command i used was grompp -f pr.mdp -n index.ndx -c box_em.pdb -p
topol.top -o box_pr.tpr
But this time i get an error like this "Atom 1 defined in multiple groups (1
& 3). "
How to overcome this error ?

Thanking you,

On Thu, Apr 9, 2009 at 10:14 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> Pawan Kumar wrote:
>> Hello sir,
>> Thanks for such a explanatory tutorial.
>> I am stuck with one error now.
>> I have protein, popc, sol and cl- in my system.
>> I have merged the sol and cl- using make_ndx.
>> But when I run grompp I get the error like this "popc not defined in the
>> index file".
>> The grompp command : grompp -f pr.mdp -c box_em.pdb -p topol.top -o
>> box_pr.tpr
> As I said last time, you'll need to give grompp the index file so that it
> can make sense of your use of the new group(s) name(s).
> Mark
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