Hi, Justin, Thanks for your advice! Do I need to add this part:
#ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name Protein [ molecules ] ; Compound #mols SOL 216 Thanks a lot! Yi On Sat, Sep 4, 2010 at 11:21 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Yi Gao wrote: > >> Hi, I used x2top to generate spc216.top. The spc216.gro file comes from >> Gromacs tutor directory. I use Gromacs 4.0.5 version. The command line is >> x2top -f scp216.gro -o scp216.top. The error message is >> >> Can not find forcefield for atom OW-1 with 2 bonds >> Can not find forcefield for atom OW-4 with 2 bonds >> Can not find forcefield for atom OW-7 with 2 bonds >> Can not find forcefield for atom OW-10 with 2 bonds >> Can not find forcefield for atom OW-13 with 2 bonds >> Can not find forcefield for atom OW-16 with 2 bonds >> Can not find forcefield for atom OW-19 with 2 bonds >> Can not find forcefield for atom OW-22 with 2 bonds >> Can not find forcefield for atom OW-25 with 2 bonds >> Can not find forcefield for atom OW-28 with 2 bonds >> Can not find forcefield for atom OW-31 with 2 bonds >> Can not find forcefield for atom OW-34 with 2 bonds >> Can not find forcefield for atom OW-37 with 2 bonds >> ... >> ------------------------------------------------------- >> Program x2top, VERSION 4.0.5 >> Source code file: x2top.c, line: 207 >> >> Fatal error: >> Could only find a forcefield type for 432 out of 648 atoms >> ------------------------------------------------------- >> >> >> I don't want to use pdb2gmx to generate *.top file, because spc216 water >> is just a part of my system. Could anyone help me to resolve this problem? >> Thanks a lot! >> >> > There is no need to do any of this. Just #include "spc.itp" in your > topology. See the manual for details, as well as: > > http://www.gromacs.org/Documentation/Include_File_Mechanism > > -Justin > > Best, >> Yi >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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