[gmx-users] x2top problem of dealing with spc216 water

[Justin A. Lemkul]

Yi Gao 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

This section is only necessary if you want to restrain the water molecules.

> ; Include generic topology for ions
> #include "ions.itp"

This section is only necessary if you will be using ions described ions.itp.

> [ system ]
> ; Name
> Protein
> [ molecules ]
> ; Compound        #mols
> SOL               216
>  

Whether or not these directives are correct for your system is something only 
you can determine.  I would encourage you to do some basic tutorial material and 
reading in Chapter 5 of the manual to understand all of these sections.

-Justin

> Thanks a lot!
>  
> Yi
> 
> On Sat, Sep 4, 2010 at 11:21 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at 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
> 
>     ========================================
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> 

-- 
========================================

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

========================================