[gmx-users] problems running grompp with protein-ligand complex
Justin A. Lemkul
jalemkul at vt.edu
Mon Dec 1 02:24:51 CET 2008
How large is the file? Most topology files should be no larger than a few kb.
Did you try to attach the file, or just paste the text into the message? The
latter would be preferred for archival purposes.
Ragnarok sdf wrote:
> Hello, I was asked to post my ligand.itp file here, but apparently the
> file is too big to be posted. I was supposed to receive a message
> telling me if the post was accepted or not. I understand that the
> administrators must be busy most of the time, so I would like to know if
> there is any other possibility to show the content of my file so that my
> problem could get solved.
> Thank you in advance.
> >Hi Fabrício,
> >> I've checked wikigromacs, but the solution given there, to simply
> erase the
> >> second default line does not suit me here. Once I do this, i mean,
> go to my
> >> ligand.itp file and put a ; before my default section, grompp does not
> >> recognize anymore that my ligand is there and gives out another
> error line.
> >Well, it's not like grompp is recognizing you have a ligand there
> >right now, is it? grompp doesn't reach the point where it realizes you
> >don't seem to have a ligand. It seems there's something wrong with the
> >topology. Better post ligand.itp, like Justin suggests, and also give
> >the error which occurs when you do comment out the defaults line in
> >the ligand topology.
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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