Justin A. Lemkul wrote: Simone Cirri wrote: > > Hi everyone, > > 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? > > I'm sorry but I don't know which procedure to follow. > Thanks in advance > > 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. >
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. The problem comes with grompp, because I get the error: Fatal error: number of coordinates in coordinate file (1JIC_dmso_water.gro, 17314) does not match topology (1JIC.top, 16454) 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). I tried to add a line: #include "dmso.itp" but I get another fatal error: Fatal error: Atomtype SD not found 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: S (sulphur in disulfide linkage) SH (sulphur in cystine) 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. How should I solve the problem, then? Thank you very much Simone Cirri simoneci...@gmail.com
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