[gmx-users] problems running grompp with protein-ligand complex

Ragnarok sdf fabracht1 at gmail.com
Mon Dec 1 04:20:57 CET 2008

Well, right after I tried to post I received a message saying that my
previous message bounced because I had exceeded the size limit of 50k.
I will try to post the file again, in case the same thing happens again I
will try to attach the file.
Thank you

How large is the file?  Most topology files should be no larger than a few
Did you try to attach the file, or just paste the text into the message?
latter would be preferred for archival purposes.


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
Thank you in advance.

>Hi Fabrício,
>> I've checked wikigromacs, but the solution given there, to simply erase
>> second default line does not suit me here. Once I do this, i mean, go to
>> 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
>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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