[EMAIL PROTECTED] wrote:
My initial input file is a model which was generated using Modeller, and
it is a part of the original structure. I am considering fragments of a
particular structure for my analysis. Could this be a possible problem for
running a simulation?? I suppose there is a problem when I try to convert
this PDB file into a .gro file. But I have no clue as to what the possible
problem could be. The format of my input PDB file is correct.
Well, you don't need a .gro file - see
http://wiki.gromacs.org/index.php/Coordinate_File#On_the_need_for_a_.gro_file
Chopping something into fragments is a great way to make chemical
nonsense, but pdb2gmx and grompp will often give you warnings and errors
about such things. Read them carefully and pay attention!
Also I tried to run a job for the original PDB structure which worked
perfectly fine.
Well that means your problem came with something you did...
Mark
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