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

[Yi Gao]

Thanks a lot!

On Sat, Sep 4, 2010 at 2:57 PM, Justin A. Lemkul <jalemkul at 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 <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
>
> ========================================
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