[gmx-users] RE: gmx-users Digest, Vol 75, Issue 23

abdul wadood wadoodbiochemist at hotmail.com
Tue Jul 6 10:48:23 CEST 2010

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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