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.htmlIt 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).