Thanks a lot!<br><br>
<div class="gmail_quote">On Sat, Sep 4, 2010 at 2:57 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="im"><br><br>Yi Gao wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">And I have ~1500 spc water. Do I only need to add #include "spc.itp" in your topology? Thanks!<br>
<br></blockquote><br></div>I will reiterate the advice in my previous message - do some tutorial material on a simple system, read Chapter 5, then proceed.<br><br>-Justin<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Yi
<div class="im"><br><br>On Sat, Sep 4, 2010 at 2:53 PM, Yi Gao <<a href="mailto:t218gy@gmail.com" target="_blank">t218gy@gmail.com</a> <mailto:<a href="mailto:t218gy@gmail.com" target="_blank">t218gy@gmail.com</a>>> wrote:<br>
<br> Hi, Justin,<br> Thanks for your advice! Do I need to add this part:<br> #ifdef POSRES_WATER<br> ; Position restraint for each water oxygen<br> [ position_restraints ]<br> ; i funct fcx fcy fcz<br>
1 1 1000 1000 1000<br> #endif<br> ; Include generic topology for ions<br> #include "ions.itp"<br> [ system ]<br> ; Name<br> Protein<br> [ molecules ]<br> ; Compound #mols<br>
SOL 216<br> Thanks a lot!<br> Yi<br><br> On Sat, Sep 4, 2010 at 11:21 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br></div>
<div>
<div></div>
<div class="h5"> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br><br><br><br> Yi Gao wrote:<br><br> Hi, I used x2top to generate spc216.top. The spc216.gro file<br>
comes from Gromacs tutor directory. I use Gromacs 4.0.5<br> version. The command line is x2top -f scp216.gro -o<br> scp216.top. The error message is<br><br> Can not find forcefield for atom OW-1 with 2 bonds<br>
Can not find forcefield for atom OW-4 with 2 bonds<br> Can not find forcefield for atom OW-7 with 2 bonds<br> Can not find forcefield for atom OW-10 with 2 bonds<br> Can not find forcefield for atom OW-13 with 2 bonds<br>
Can not find forcefield for atom OW-16 with 2 bonds<br> Can not find forcefield for atom OW-19 with 2 bonds<br> Can not find forcefield for atom OW-22 with 2 bonds<br> Can not find forcefield for atom OW-25 with 2 bonds<br>
Can not find forcefield for atom OW-28 with 2 bonds<br> Can not find forcefield for atom OW-31 with 2 bonds<br> Can not find forcefield for atom OW-34 with 2 bonds<br> Can not find forcefield for atom OW-37 with 2 bonds<br>
...<br> -------------------------------------------------------<br> Program x2top, VERSION 4.0.5<br> Source code file: x2top.c, line: 207<br><br> Fatal error:<br> Could only find a forcefield type for 432 out of 648 atoms<br>
-------------------------------------------------------<br><br><br> I don't want to use pdb2gmx to generate *.top file, because<br> spc216 water is just a part of my system. Could anyone help<br>
me to resolve this problem? Thanks a lot!<br><br><br> There is no need to do any of this. Just #include "spc.itp" in<br> your topology. See the manual for details, as well as:<br><br> <a href="http://www.gromacs.org/Documentation/Include_File_Mechanism" target="_blank">http://www.gromacs.org/Documentation/Include_File_Mechanism</a><br>
<br> -Justin<br><br> Best,<br> Yi<br><br><br> -- ========================================<br><br> Justin A. Lemkul<br> Ph.D. Candidate<br> ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br> Department of Biochemistry<br> Virginia Tech<br> Blacksburg, VA<br></div></div> jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> <<a href="http://vt.edu/" target="_blank">http://vt.edu/</a>> | (540) 231-9080
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<div class="h5"><br>-- <br>========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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