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

[Justin A. Lemkul]

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 <t218gy at gmail.com 
> <mailto:t218gy at 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 <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

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