Dear gmx-usrs
Thanks you all for you valuable suggestion. Unfortunately, the problem is still
exist.
I add the hydrogen to LEU2 but then the error come for the next amino acid.
I also used the -ignh but the error was same.
I dont understand one thing which is that when I used simply Pro instead of
NPRO which is N ternimal amino acid and SER instead of CSER which is C-terminal
amino acid in my protein. Then no error come and pdb2gmx produced top file and
other file without any error. However, the message come that
N-terminus: none
C-terminus: none
I am using gromacs 4.0.5
Now, I am in doubt that I am going in the right way or I have to modify PRO
with NPRO and SER with CSER.
Your help in this respect will by highly appreciated.
Thanks in advance
many regards
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