Justin A. Lemkul wrote:<br><br><blockquote style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;" class="gmail_quote">Simone Cirri wrote:<br><br>Hi everyone,<br><br>I need to run a simulation of a protein in a water/DMSO mixture. I can't quite understand how should I do this... should I normally solvate the protein with water and then replace a certain number of water molecules (according to the needed % of DMSO) with DMSO molecules? But in this case, how should I do it? Is there a way of replacing solvent molecules with other solvent molecules, but of a different type?<br>
<br>I'm sorry but I don't know which procedure to follow.<br>Thanks in advance<br><br>The easiest way I can think of is to define the box around your protein, use genbox -ci -nmol to insert the desired number of DMSO molecules, and then fill the box with water. You may have to tweak the box size or use genbox -maxsol to get the desired concentration.<br>
</blockquote><br>Hi Justin, I've tried your method. More or less, it works: I manage to insert the exact desired number of DMSO molecules, and when I fill the box with water, I get slightly less molecules that the ones I calculated, but I think I can ignore that.<br>
The problem comes with grompp, because I get the error:<br><br>Fatal error:<br>number of coordinates in coordinate file (1JIC_dmso_water.gro, 17314)<br> does not match topology (1JIC.top, 16454)<br><br>because, evidently, the .top file does not contain any trace of the 215 DMSO molecules I added (215 x 4 = 860, which is the difference of coordinates between the .gro file and the .top file).<br>
I tried to add a line:<br>#include "dmso.itp"<br>but I get another fatal error:<br><br>Fatal error:<br>Atomtype SD not found<br><br>due to the fact that I'm using the AMBER99 forcefield. In fact, this forcefield (as I've seen in the .atp file) only contains 2 types of S:<br>
S (sulphur in disulfide linkage)<br>SH (sulphur in cystine)<br>and I guess that none of them is the right one... so I don't think I can simply rename the SD in the dmso.itp file to S, for example.<br>How should I solve the problem, then?<br>
Thank you very much<br><br>Simone Cirri<br><br><a href="mailto:simonecirri@gmail.com">simonecirri@gmail.com</a><br>