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Dear gmx-usrs<br><br>Thanks you all for you valuable suggestion. Unfortunately, the problem is still exist.<br>I add the hydrogen to LEU2 but then the error come for the next amino acid.<br><br>I also used the -ignh but the error was same.<br><br>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 <br><br>N-terminus: none<br>C-terminus: none<br><br>I am using gromacs 4.0.5<br><br>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.<br><br>Your help in this respect will by highly appreciated.<br><br>Thanks in advance<br><br>many regards<br> <br /><hr />Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. <a href='http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1' target='_new'>Learn more.</a></body>
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