>> Hi,<br>>> I wanna keep crystallographic water with tip4p model for md simulation but when I use pdb2gmx even if I set "-water tip4p" it protonates oxygens to spc water model instead.<br>>> Is there any way to replace spc water molecules with tip4p water molecules in the same orientation?<br>
><br>>What's your GROMACS version and command line?<br>><br>>> Btw what happen if I'll keep 2 types of water models in one simulation?<br>><br>>Your reviewers will giggle.<br>><br>>Mark<br>
<br>Hi<br>I’m using following lines to prepare structure<br><br>pdb2gmx -f 1KEH.pdb -o 1keh.gro -p 1keh.top -ff oplsaa -water tip4p<br>editconf -f 1keh.gro -d 1 -c -bt cubic -o 1keh.box.gro<br>genbox -cp 1keh.box.gro -cs tip4p.gro -o 1keh.sol.gro -p 1keh.top<br>
<br>after this in 1keh.sol.gro there are 2 types of water like<br> 1078HO4 HW112050 5.331 6.748 7.575<br> 1078HO4 HW212051 5.413 6.666 7.459<br> 1078HO4 HW312052 5.413 6.748 7.517<br> 1079HO4 OW12053 7.630 6.590 7.095<br>
1079HO4 HW112054 7.630 6.671 7.037<br> 1079HO4 HW212055 7.630 6.508 7.037<br> 1079HO4 HW312056 7.630 6.590 7.095<br> 1080HO4 OW12057 3.861 4.563 2.433<br><br>and like <br> 1083SOL OW12069 1.736 0.839 0.257<br>
1083SOL HW112070 1.777 0.781 0.322<br> 1083SOL HW212071 1.643 0.831 0.274<br> 1083SOL MW12072 1.730 0.831 0.267<br> 1084SOL OW12073 1.602 0.771 1.252<br> 1084SOL HW112074 1.557 0.838 1.303<br>
1084SOL HW212075 1.690 0.807 1.238<br> 1084SOL MW12076 1.608 0.784 1.256<br>as I can understand pdb2gmx converted crystallographic O into H2O with additional H in the same place as O instead of additional M near O<br>
how can it be fixed? <br>