[gmx-users] cyclic peptides

andrea spitaleri spitaleri.andrea at hsr.it
Fri Oct 20 13:59:37 CEST 2006

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



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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Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)

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