[gmx-users] cyclic peptides

[Giacomo Bastianelli]

Hi Andrea,

this is my input for the minimization:

#Minimisation
grompp -f EM.mdp -c 1KAL_SOLV.pdb -p 1kal.top -o 1KAL_MINI.tpr mdrun -s 
1KAL_MINI.tpr -o 1KAL_MINI.trr -x 1KAL_MINI.xtc -c 1KAL_MINI.pdb -v -e 
1KAL_MINI.edr

Giacomo

andrea spitaleri wrote:
> Hi Giacomo,
> you are using the flag -c twice. Check your input line in the shell. 
> See mdrun -h for more information.
> It should be something like:
> mdrun -s file.tpr -o file.trr -c file.pdb
> probably you have
> mdrun -s file.tpr -o file.trr -c -c file.pdb
> -------------------------------^
> a typo error
>
> Regards
>
>
> Andrea
>
> Giacomo Bastianelli wrote:
>> Hi David,
>>
>> is there an error in the souce code file????
>>
>> ps.sorry if the question is stupid but I am very
>> naive to bioinformatic as well...
>> Giacomo
>>
>> David van der Spoel wrote:
>>> Giacomo Bastianelli wrote:
>>>> Hi Tsjerk,
>>>>
>>>> I have just fixed the problem of cyclic (manually deleted some bonds
>>>> that gromacs added...), I got everything ready for the minimization
>>>> step after genbox.
>>>> I run it and it says:
>>>>
>>>> Program grompp, VERSION 3.3
>>>> Source code file: statutil.c, line: 549
>>>>
>>>> Fatal error:
>>>> Double command line argument -c
>>>>
>>>> Is there anything wrong with my inputs?
>>>>
>>>> thanks a lot
>>>>
>>> yes. it is exactly what it says.
>>>
>>
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>