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<P>Dear all,</P>
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<P>I used beta version of PRODRG to produce G43a1 ff for a single DPPC molecule. When I try to make geometry optimisation, always I am facing with large Fmax values and large 1-4 interaction value.</P>
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<P>When I visualize the *.gro file of the output, it seems some atom types are changed!</P>
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<P>I am attaching input pdb file and output gro file.</P>
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<P>What is the wrong thing here? Could any body tell me please?</P>
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<P>Serdar</P>
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<P>input pdb file:</P>
<P> </P><FONT size=2>
<P>TITLE Gyas ROwers Mature At Cryogenic Speed</P>
<P>REMARK THIS IS A SIMULATION BOX</P>
<P>CRYST1 45.149 45.149 45.149 90.00 90.00 90.00 P 1 1</P>
<P>MODEL 1</P>
<P>HETATM 1 N1 MOL 1 34.444 18.233 25.460 1.00 0.00</P>
<P>HETATM 2 C7 MOL 1 35.570 19.239 25.501 1.00 0.00</P>
<P>HETATM 3 C6 MOL 1 35.017 16.871 25.137 1.00 0.00</P>
<P>HETATM 4 C5 MOL 1 33.796 18.184 26.832 1.00 0.00</P>
<P>HETATM 5 C2 MOL 1 33.479 18.667 24.357 1.00 0.00</P>
<P>HETATM 6 C3 MOL 1 32.028 18.158 24.509 1.00 0.00</P>
<P>HETATM 7 O4 MOL 1 31.392 18.891 25.581 1.00 0.00</P>
<P>HETATM 8 P8 MOL 1 29.882 18.565 25.912 1.00 0.00</P>
<P>HETATM 9 O9 MOL 1 29.334 17.523 25.021 1.00 0.00</P>
<P>HETATM 10 O11 MOL 1 29.292 19.999 25.571 1.00 0.00</P>
<P>HETATM 11 C12 MOL 1 28.661 20.699 26.667 1.00 0.00</P>
<P>HETATM 12 C13 MOL 1 27.887 21.958 26.219 1.00 0.00</P>
<P>HETATM 13 O31 MOL 1 26.485 21.650 25.948 1.00 0.00</P>
<P>HETATM 14 C32 MOL 1 26.067 20.880 24.918 1.00 0.00</P>
<P>HETATM 15 O46 MOL 1 26.794 20.369 24.088 1.00 0.00</P>
<P>HETATM 16 C33 MOL 1 24.556 20.779 24.890 1.00 0.00</P>
<P>HETATM 17 C34 MOL 1 23.968 21.111 23.497 1.00 0.00</P>
<P>HETATM 18 C35 MOL 1 22.446 21.361 23.564 1.00 0.00</P>
<P>HETATM 19 C36 MOL 1 21.866 21.656 22.162 1.00 0.00</P>
<P>HETATM 20 C37 MOL 1 20.364 22.006 22.249 1.00 0.00</P>
<P>HETATM 21 C38 MOL 1 19.701 22.059 20.856 1.00 0.00</P>
<P>HETATM 22 C39 MOL 1 18.202 22.412 20.975 1.00 0.00</P>
<P>HETATM 23 C40 MOL 1 17.447 22.130 19.660 1.00 0.00</P>
<P>HETATM 24 C41 MOL 1 15.956 22.512 19.778 1.00 0.00</P>
<P>HETATM 25 C42 MOL 1 15.163 22.060 18.534 1.00 0.00</P>
<P>HETATM 26 C43 MOL 1 13.677 22.462 18.642 1.00 0.00</P>
<P>HETATM 27 C44 MOL 1 12.876 21.978 17.413 1.00 0.00</P>
<P>HETATM 28 C45 MOL 1 11.392 22.382 17.522 1.00 0.00</P>
<P>HETATM 29 C1 MOL 1 10.593 21.928 16.284 1.00 0.00</P>
<P>HETATM 30 C8 MOL 1 9.112 22.333 16.402 1.00 0.00</P>
<P>HETATM 31 C14 MOL 1 28.585 22.745 25.083 1.00 0.00</P>
<P>HETATM 32 O15 MOL 1 28.067 24.102 25.033 1.00 0.00</P>
<P>HETATM 33 C16 MOL 1 26.879 24.330 24.441 1.00 0.00</P>
<P>HETATM 34 O30 MOL 1 26.330 23.544 23.703 1.00 0.00</P>
<P>HETATM 35 C17 MOL 1 26.294 25.661 24.826 1.00 0.00</P>
<P>HETATM 36 C18 MOL 1 24.751 25.657 24.891 1.00 0.00</P>
<P>HETATM 37 C19 MOL 1 24.067 25.811 23.515 1.00 0.00</P>
<P>HETATM 38 C20 MOL 1 22.542 25.943 23.704 1.00 0.00</P>
<P>HETATM 39 C21 MOL 1 21.791 26.100 22.367 1.00 0.00</P>
<P>HETATM 40 C22 MOL 1 20.287 26.328 22.625 1.00 0.00</P>
<P>HETATM 41 C23 MOL 1 19.486 26.449 21.314 1.00 0.00</P>
<P>HETATM 42 C24 MOL 1 17.984 26.636 21.604 1.00 0.00</P>
<P>HETATM 43 C25 MOL 1 17.163 26.715 20.301 1.00 0.00</P>
<P>HETATM 44 C26 MOL 1 15.652 26.784 20.601 1.00 0.00</P>
<P>HETATM 45 C27 MOL 1 14.825 26.856 19.302 1.00 0.00</P>
<P>HETATM 46 C28 MOL 1 13.315 26.838 19.610 1.00 0.00</P>
<P>HETATM 47 C29 MOL 1 12.478 26.954 18.320 1.00 0.00</P>
<P>HETATM 48 C9 MOL 1 10.969 26.915 18.635 1.00 0.00</P>
<P>HETATM 49 C10 MOL 1 10.129 27.155 17.369 1.00 0.00</P>
<P>HETATM 50 O10 MOL 1 29.702 18.159 27.328 1.00 0.00</P>
<P>TER</P>
<P>ENDMDL</P></FONT>
<P> </P>
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<P>output pdb file</P>
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<P> </P>
<P><FONT size=2>GROningen MAchine for Chemical Simulation in water</FONT></P>
<P><FONT size=2>50</FONT></P>
<P><FONT size=2>1MOL C31 1 3.445 1.823 2.546</FONT></P>
<P><FONT size=2>1MOL C30 2 3.557 1.924 2.550</FONT></P>
<P><FONT size=2>1MOL C29 3 3.502 1.687 2.514</FONT></P>
<P><FONT size=2>1MOL C28 4 3.379 1.818 2.683</FONT></P>
<P><FONT size=2>1MOL C27 5 3.347 1.867 2.435</FONT></P>
<P><FONT size=2>1MOL C26 6 3.203 1.816 2.451</FONT></P>
<P><FONT size=2>1MOL C25 7 3.139 1.889 2.558</FONT></P>
<P><FONT size=2>1MOL C24 8 2.988 1.856 2.591</FONT></P>
<P><FONT size=2>1MOL C23 9 2.933 1.752 2.502</FONT></P>
<P><FONT size=2>1MOL C22 10 2.929 2.000 2.557</FONT></P>
<P><FONT size=2>1MOL C21 11 2.866 2.070 2.667</FONT></P>
<P><FONT size=2>1MOL C20 12 2.788 2.195 2.622</FONT></P>
<P><FONT size=2>1MOL C19 13 2.648 2.165 2.595</FONT></P>
<P><FONT size=2>1MOL C18 14 2.607 2.088 2.492</FONT></P>
<P><FONT size=2>1MOL C17 15 2.679 2.037 2.409</FONT></P>
<P><FONT size=2>1MOL C15 16 2.456 2.078 2.489</FONT></P>
<P><FONT size=2>1MOL O16 17 2.397 2.111 2.350</FONT></P>
<P><FONT size=2>1MOL O14 18 2.245 2.136 2.356</FONT></P>
<P><FONT size=2>1MOL C13 19 2.187 2.166 2.216</FONT></P>
<P><FONT size=2>1MOL C12 20 2.036 2.201 2.225</FONT></P>
<P><FONT size=2>1MOL O11 21 1.970 2.206 2.086</FONT></P>
<P><FONT size=2>1MOL P8 22 1.820 2.241 2.097</FONT></P>
<P><FONT size=2>1MOL O9 23 1.745 2.213 1.966</FONT></P>
<P><FONT size=2>1MOL O10 24 1.596 2.251 1.978</FONT></P>
<P><FONT size=2>1MOL O7 25 1.516 2.206 1.853</FONT></P>
<P><FONT size=2>1MOL C6 26 1.368 2.246 1.864</FONT></P>
<P><FONT size=2>1MOL C5 27 1.288 2.198 1.741</FONT></P>
<P><FONT size=2>1MOL N4 28 1.139 2.238 1.752</FONT></P>
<P><FONT size=2>1MOL C2 29 1.059 2.193 1.628</FONT></P>
<P><FONT size=2>1MOL C3 30 0.911 2.233 1.640</FONT></P>
<P><FONT size=2>1MOL C1 31 2.859 2.273 2.508</FONT></P>
<P><FONT size=2>1MOL C32 32 2.806 2.412 2.503</FONT></P>
<P><FONT size=2>1MOL O33 33 2.688 2.433 2.444</FONT></P>
<P><FONT size=2>1MOL C34 34 2.633 2.354 2.370</FONT></P>
<P><FONT size=2>1MOL O35 35 2.629 2.566 2.483</FONT></P>
<P><FONT size=2>1MOL C36 36 2.475 2.566 2.489</FONT></P>
<P><FONT size=2>1MOL C37 37 2.407 2.581 2.352</FONT></P>
<P><FONT size=2>1MOL C38 38 2.254 2.594 2.370</FONT></P>
<P><FONT size=2>1MOL C39 39 2.179 2.610 2.237</FONT></P>
<P><FONT size=2>1MOL C40 40 2.029 2.633 2.262</FONT></P>
<P><FONT size=2>1MOL C41 41 1.949 2.645 2.131</FONT></P>
<P><FONT size=2>1MOL C42 42 1.798 2.664 2.160</FONT></P>
<P><FONT size=2>1MOL C43 43 1.716 2.671 2.030</FONT></P>
<P><FONT size=2>1MOL C44 44 1.565 2.678 2.060</FONT></P>
<P><FONT size=2>1MOL C45 45 1.482 2.686 1.930</FONT></P>
<P><FONT size=2>1MOL C46 46 1.332 2.684 1.961</FONT></P>
<P><FONT size=2>1MOL C47 47 1.248 2.695 1.832</FONT></P>
<P><FONT size=2>1MOL C48 48 1.097 2.692 1.864</FONT></P>
<P><FONT size=2>1MOL C49 49 1.013 2.715 1.737</FONT></P>
<P><FONT size=2>1MOL C50 50 2.970 1.816 2.733</FONT></P>
<P><FONT size=2>4.51490 4.51490 4.51490</FONT></P>
<P><FONT size=2> </FONT></P>
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<P><BR><BR>--- Justin A. Lemkul <I><jalemkul@vt.edu></I> schrieb am <B>Mo, 7.7.2008:<BR></P>
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: rgb(16,16,255) 2px solid">Von: Justin A. Lemkul <jalemkul@vt.edu><BR>Betreff: Re: [gmx-users] lipid itp problem<BR>An: durdagis@yahoo.de, "Gromacs Users' List" <gmx-users@gromacs.org><BR>Datum: Montag, 7. Juli 2008, 14:06<BR><BR><PRE>Please make sure to include the gmx-users list on correspondence;
someone else may have a useful idea.
It looks to me that your "input.pdb" is badly broken. Is this what
PRODRG generated? Are you using this structure for anything? Where are
the coordinates for your lipid bilayer coming from?
I would suggest starting over with the minimization - take the .pdb file
that PRODRG generates (united-atom representation, as you've tried to
use here), center it in a large box to avoid PBC effects (using editconf
-c), and try again.
Just a general thought as well - it has long been said over this list
that ffgmx should not be used for any new production simulations. It is
deprecated and the results from it may not be as reliable as one of the
newer, Gromos96 force fields. I would suggest using the PRODRG beta
server to generate parameters under Gromos96 43a1. None of this is
likely the root cause of your problem, however.
-Justin========================================</PRE></BLOCKQUOTE></B></TD></TR></TBODY></TABLE></DIV></td></tr></table><br>
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