jo hanna wrote: > I have been trying for some time now to model with 2 ligands and 1 water > molecule and I feel that I have tried everything from the list, faq and > tutorials and not got very far. > I have posted a number of questions to the list but can still not get > this to work, properly!
In order to be able to help you, you need to post your full inputs. See http://salilab.org/modeller/manual/node11.html It is essentially impossible to reproduce your problem if you only post part of your alignment.
If your sequences are confidential or just rather large, you can send them directly to me rather than the list.
> I cannot type w at the end > of the sequence alignment however as this causes modeller to fail with > an out of range error.
I would also be interested in seeing the input files that result in this error, as I'm not sure what you're doing wrong here (but Modeller should certainly be fixed to give a more understandable error message in this case).
Ben Webb, Modeller Caretaker