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

[Yi Gao]

And I have ~1500 spc water. Do I only need to add #include "spc.itp" in your
topology? Thanks!

Yi

On Sat, Sep 4, 2010 at 2:53 PM, Yi Gao <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>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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>
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