[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.
>  >
>  >Cheers,
>  >
>  >Tsjerk
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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