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Hello,<div><br></div><div>While I am simulating my simulations, I encountered below error. </div><div>I have pdb file which is:</div><div><br></div><div><div>HEADER PROTEIN</div><div>TITLE (5,5) Nanotube (1,1,80) replication</div><div>AUTHOR TubeGen 3.3, J T Frey, University of Delaware</div><div>EXPDTA THEORETICAL MODEL</div><div>ATOM 1 C UNK 1 3.410 0.000 -98.494 1.00 0.00</div><div>ATOM 2 C UNK 1 3.113 1.390 -98.494 1.00 0.00</div><div>ATOM 3 C UNK 1 2.758 2.004 -97.263 1.00 0.00</div><div>ATOM 4 C UNK 1 1.702 2.954 -97.263 1.00 0.00</div><div>ATOM 5 C UNK 1 1.054 3.243 -98.494 1.00 0.00</div><div>ATOM 6 C UNK 1 -0.360 3.391 -98.494 1.00 0.00</div><div>ATOM 7 C UNK 1 -1.054 3.243 -97.263 1.00 0.00</div><div>ATOM 8 C UNK 1 -2.284 2.532 -97.263 1.00 0.00</div><div>ATOM 9 C UNK 1 -2.758 2.004 -98.494 1.00 0.00</div><div>...<br><div>CONECT 1596 1595 1597</div><div>CONECT 1597 1576 1596 1598</div><div>CONECT 1598 1579 1597 1599</div><div>CONECT 1599 1598 1600</div><div>CONECT 1600 1581 1599</div><div>MASTER 0 0 0 0 0 0 0 0 1600 0 1600 0</div><div>END </div><div><br></div><div><br></div><div>But by using text editor, I change an atom with another atom.</div><div>And I created .top and .gro files respectively.</div><div>( my sample is basically similar to Christopher Stiles' work, http://cs86.com/CNSE/SWNT.htm)</div><div><br></div><div><br></div><div>After I run my simulation, it gives the error:</div><div><br></div><div><br></div><div><br></div><div><div>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#</div><div>checking input for internal consistency...</div><div>calling cpp...</div><div>processing topology...</div><div>Generated 1282 of the 1485 non-bonded parameter combinations</div><div>WARNING 1 [file "cnt_500.top", line 72238]:</div><div> No default Angle types, using zeroes</div><div>WARNING 2 [file "cnt_500.top", line 72238]:</div><div> No default Angle types for perturbed atoms, using normal values</div><div>WARNING 3 [file "cnt_500.top", line 72239]:</div><div> No default Angle types, using zeroes</div><div>WARNING 4 [file "cnt_500.top", line 72239]:</div><div> No default Angle types for perturbed atoms, using normal values</div><div>WARNING 5 [file "cnt_500.top", line 72240]:</div><div> No default Angle types, using zeroes</div><div>WARNING 6 [file "cnt_500.top", line 72240]:</div><div> No default Angle types for perturbed atoms, using normal values</div><div>WARNING 7 [file "cnt_500.top", line 72241]:</div><div> No default Angle types, using zeroes</div><div>WARNING 8 [file "cnt_500.top", line 72241]:</div><div> No default Angle types for perturbed atoms, using normal values</div><div>WARNING 9 [file "cnt_500.top", line 72242]:</div><div> No default Angle types, using zeroes</div><div>WARNING 10 [file "cnt_500.top", line 72242]:</div><div> No default Angle types for perturbed atoms, using normal values</div><div>Cleaning up temporary file gromppYFxvHw</div><div>-------------------------------------------------------</div><div>Program grompp_mpi, VERSION 3.3.1</div><div>Source code file: fatal.c, line: 416</div><div><br></div><div>Fatal error:</div><div>Too many warnings, grompp_mpi terminated</div><div>-------------------------------------------------------</div><div><br></div><div><br></div><div>Without changing my pdb file, there was no error but after I can an atom with another, I got above error.</div><div>Is there anyone who had same problem before? I will really appreciate if you can help me. </div><div><br></div><div>Thank you,</div><div>Kasim</div></div></div></div> <br /><hr />Hotmail: Trusted email with powerful SPAM protection. <a href='http://clk.atdmt.com/GBL/go/177141665/direct/01/' target='_new'>Sign up now.</a></body>
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