Thanks a lot! On Sat, Sep 4, 2010 at 2:57 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Yi Gao wrote: > >> And I have ~1500 spc water. Do I only need to add #include "spc.itp" in >> your topology? Thanks! >> >> > > I will reiterate the advice in my previous message - do some tutorial > material on a simple system, read Chapter 5, then proceed. > > -Justin > > Yi >> >> >> On Sat, Sep 4, 2010 at 2:53 PM, Yi Gao <t21...@gmail.com <mailto: >> t21...@gmail.com>> wrote: >> >> 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 >> <mailto: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 <http://vt.edu/> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> > -- > ======================================== > > 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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