[gmx-users] cyclic peptides

[Giacomo Bastianelli]

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

Giacomo



Tsjerk Wassenaar wrote:
> Hi Giacomo,
>
> Did pdb2gmx finish without errors? You have a cyclic peptide and
> pdb2gmx will normally add N- and C-termini. You can override that by
> using the -ter flag on the pdb2gmx command line and select "none" for
> both termini. Then you have to edit the .top file and add the required
> bonds, angles and dihedrals to make the peptide cyclic. Gromacs can't
> do that for you (at present; maybe a -cyclic option in pdb2gmx for
> peptides might come in handy if there is substantial demand for
> simulations of cyclic peptides).
>
> But I'm a bit concerned about the error genbox gives. It complains
> that it can't find the topology you say you want it to read (-p
> 1KAL.top). If that is the topology you think you've generated with
> pdb2gmx, check it's output and check your directory listing.
>
> Best,
>
> Tsjerk
>
>
> On 10/20/06, Giacomo Bastianelli <gbastian at pasteur.fr> wrote:
>> I have the top file and I create the topology file using pdb2gmx.
>> I then generate with editconf the water box.
>>
>> after that genbox fails...
>>
>> thanks!
>>
>> giacomo
>>
>> Tsjerk Wassenaar wrote:
>> > Hi Giacomo,
>> >
>> > You have to provide more information than that. Do you actually have a
>> > file 1KAL.top (I expect not). How did you (or do you think you did)
>> > create the topology? Using pdb2gmx? Please summarize what you did so
>> > far and to get to the point where genbox fails on you?
>> >
>> > Best,
>> >
>> > Tsjerk
>> >
>> > On 10/19/06, Giacomo Bastianelli <gbastian at pasteur.fr> wrote:
>> >> I have to run a md of a cyclic peptide.
>> >> Does anybody know how to modify to have
>> >> it running...
>> >>
>> >> actually I corrected the file and then run it.
>> >> then I arrive at the step "genbox" and it write
>> >> the top file but it says:
>> >>
>> >> file input/output error: 1KAL.top
>> >>
>> >> and then I keep having problems for the next steps...
>> >>
>> >> thanks
>> >>
>> >> giacomo
>> >>
>> >>
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