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