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

[Yi Gao]

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> 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
>
> ========================================
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