[gmx-users] Re: Re: crystallographic water to tip4p model

[Павел Кудрявцев]

>> 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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