Dear Mark, Thank you for your reply which solved my problem. I want to add something for all gmx-users. I looked at the force field folders in share/top in which possible usable water models for each force field are listed in watermodels.dat files. If you want to use a different model that is not included in the list, look at the "pdb2gmx" title at the end of the manual.
trevor On 10/01/2011 2:41 AM, trevor brown wrote: > Dear friends, > My run commands are below. It works without any error. > However if I add -water tip3p at the end of pdg2gmx ... line it causes > an error (Atomtpe HW not found) at grompp time. > Could anyone explain the difference? > trevor > pdb2gmx -ignh -f XXX.pdb -o fws.gro -p fws.top > editconf -f fws.gro -bt dodecahedron -d 1.0 > editconf -f out.gro -o fws_ctr.gro -center 1.7 1.7 1.2 > genbox -cp fws_ctr.gro -cs spc216.gro -o fws_b4em.gro -p fws.top Not all water models are intended to go with all force fields. G43a1 does not define the HW atom type used for TIP3P water, possibly by Berk's design :-). I don't remember whether it's reasonable to want to use TIP3P with the GROMOS forcefields, but presumably SPC water will work with them. Mark
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