Hi, Mark,<br>Thanks for reply.<br><br><br><div class="gmail_quote">On Sun, Mar 9, 2008 at 1:41 AM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="Ih2E3d">Liu Shiyong wrote:<br>
> Hi, all<br>
><br>
> My purpose is to get the binding energy by gromacs.<br>
<br>
</div>You can't do this without water. The binding energy involves displacing<br>
water interactions.<br>
<div class="Ih2E3d"></div></blockquote><div> <br> Yes, But I just tried to get the binding energy by minimizing protein-protein decoy without water. <br><br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="Ih2E3d"><br>
> I tried to minimize protein-protein docking decoy by using gromacs<br>
> without water. But after being minimized, the ligand ran away from<br>
> receptor.<br>
<br>
</div>"ran away" during what calculation?<br>
<div class="Ih2E3d"></div></blockquote><br> During minimizing ...<br>The following is my script. r-l_1.pdb is a protein-protein decoy structure.<br><br>pdb2gmx -ff oplsaa -f r-l_1.pdb -p r-l_1.top -o r-l_1.gro -missing > output.pdb2gmx 2>&1 &<br>
grompp -f em.mdp -c r-l_1.gro -p r-l_1.top -o input.tpr > output.grompp 2>&1 &<br>mdrun -nice 0 -v -s input.tpr -o minim_traj.trr -c minimized.gro -e minim_ener.edr > output.mdrun 2>&1 &<br><br>
<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d"><br>
> That's not what I expected . I just want to relax the protein-protein<br>
> interface due to some atom-atom contact crash .<br>
<br>
</div>That's what position-restrained EM or MD is for.<br>
<div class="Ih2E3d"></div></blockquote><div><br> Yes, I will try position-restrained EM. Thanks for suggestion. <br><br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="Ih2E3d"><br>
> By the way, I found the net charge is not zero after adding H atoms on<br>
> complex by pdb2gmx. Can I solve the non-zero net charge problem by<br>
> adding H atom on receptor and ligand<br>
><br>
> separately?<br>
<br>
</div>Depends what's causing the non-zero charge. Integral non-zero charge is<br>
different from non-integral. Some integral charges are sensible, some<br>
aren't.<br>
</blockquote><div><br> The method of adding H atom that I used is <br>pdb2gmx -ff oplsaa -f r-l_1.pdb -p r-l_1.top -o r-l_1.gro -missing > output.pdb2gmx 2>&1 &<br> It added all H atom on receptor and ligand at the same time. Is it a possible reason for Integral non-zero charge ?<br>
I want to try to add H atom on receptor and ligand , separately. <br><br>Do you know how to add H atom on receptor and ligand , separately , and combine them into one input file as minimizing ? <br> <br>If I was wrong, please point out my mistake. Thanks.<br>
<br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>
Mark<br>
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</blockquote></div><br><br clear="all"><br>-- <br>Shiyong Liu<br>Research Assistant<br>center for bioinformatics in the university of kansas<br>Lab: (785)864-1962<br>Email: <a href="mailto:syliu@ku.edu">syliu@ku.edu</a> (<a href="mailto:shiyongliu@ku.edu">shiyongliu@ku.edu</a> or <a href="mailto:liushiyong@ku.edu">liushiyong@ku.edu</a>)<br>
Homepage: <a href="http://www.people.ku.edu/~syliu">http://www.people.ku.edu/~syliu</a><br>Lab: <a href="http://vakser.bioinformatics.ku.edu/people">http://vakser.bioinformatics.ku.edu/people</a><br>Phone: (785) 864-1962