[gmx-users] How can I ...?

[Mark Abraham]

On 25/12/2010 11:21 PM, mohsen ramezanpour wrote:
> Dear All
> I want to generate .top and .gro files for protein-ligand complex.
> there are many problems,can every body guide me?
> Actually it is my M.sc thesis and it has taken much time of me.

Yep, research is difficult and time-consuming and hard to do without a 
live person of whom to ask questions in real time.

> problems:
> 1-after using PRODRG server the vector boxes for  are not the same
> 2-ligand's coordinates change very much,then my structure is not the 
> original one that I wanted(I think it is because of box vector)
> 3-there are a few atom types which is not familiar for grompp
>
> Actually I don't know what I can do with this condition
> If any of you can generate them for me please say me to send 
> complex.pdb file in his/her email.

Sounds like you are embarked on a 
http://www.gromacs.org/Documentation/How-tos/Parameterization problem 
that should only be attempted by experienced users who can put in the 
time to do it properly. At the very least, you should do all the 
tutorial material you can find, and do some other MD study before 
needing to worry about developing novel parameters.

Mark