[gmx-users] pdb2gmx -water-> grompp

[Justin A. Lemkul]

Paymon Pirzadeh wrote:
> I checked all the force-fields available in the GROAMCS. None of them
> have the #2 combination rule which matches my water model! Any
> alternatives (rather than changing my water model)?
> 

The CHARMM27 and AMBER force fields use combination rule #2.

-Justin

> Payman
> 
> 
> 
> 
> On Tue, 2009-08-18 at 18:52 -0400, Justin A. Lemkul wrote:
>> Paymon Pirzadeh wrote:
>>> That was very helpful! But I realized a problem. The OPLSaa uses the
>>> combination rule #3 in [ defaults ] while my water model uses #2. Now if
>>> I comment out my water model's combination, I am not sure what I am
>>> going to face! Any comments?
>>>
>> Then I would say that your water model's combination rule is inconsistent with 
>> the method of nonbonded calculations in OPLS.  It appears that the only 
>> difference between combination rules 2 and 3 comes when a specific interaction 
>> is not defined in the [nonbond_params] section.  The specifics of these 
>> combination rules are given in manual section 5.3.3.
>>
>> -Justin
>>
>>> Payman
>>>
>>>
>>>
>>>
>>> On Tue, 2009-08-18 at 18:19 -0400, Justin A. Lemkul wrote:
>>>> Paymon Pirzadeh wrote:
>>>>> Well,
>>>>> I changed the topology file of the system and manually typed the .itp of
>>>>> my own water model. Just a reminder that I have used my own water
>>>>> model's .itp file successfully in pure water systems. This .itp file
>>>>> starts from [ defaults ] and contains all information needed. But when
>>>>> it comes to grompp, the following error appears:
>>>>>
>>>>> Program grompp_d_mpi, VERSION 4.0.5
>>>>> Source code file: topio.c, line: 415
>>>>>
>>>>> Fatal error:
>>>>> Syntax error - File sixsitewater.itp, line 6
>>>>> Last line read:
>>>>> '[ defaults ]'
>>>>> Invalid order for directive defaults
>>>>>
>>>> The only time that [defaults] should appear is in the force field that you are 
>>>> calling (i.e., ffoplsaa.itp):
>>>>
>>>> http://oldwiki.gromacs.org/index.php/Errors#Invalid_order_for_directive_defaults
>>>>
>>>> -Justin
>>>>
>>>>> I am trying to use this water model with OPLSaa. what kind of directive
>>>>> am I missing? 
>>>>>
>>>>> Payman
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Tue, 2009-08-18 at 16:05 -0400, Justin A. Lemkul wrote:
>>>>>> Paymon Pirzadeh wrote:
>>>>>>> Hello,
>>>>>>> I am trying to use a different water model for my proteins (using oplsaa
>>>>>>> force field). I use the .itp file which I developed, but pdb2gmx does
>>>>>>> not accept it. I am a bit confused on how I can make my water model work
>>>>>>> with OPLSaa. Based on what I saw from spc.itp or other samples, do I
>>>>>>> need to change the names of my particles in my water .itp file by
>>>>>>> including _FF_OPLS?
>>>>>> I don't know how pdb2gmx decides how to recognize water models; it may be 
>>>>>> hard-coded.  In any case, your atom types have to be consistent with OPLS 
>>>>>> standards; as for whether or not you need the #ifdef _FF_OPLS in your .itp file, 
>>>>>> you may not need it if OPLS is the only force field with which it will be used. 
>>>>>>   The #ifdef blocks just prevent a GROMOS system from trying to recognize OPLS, etc.
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>>> Regards,
>>>>>>>
>>>>>>> Payman 
>>>>>>>
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>>>
> 
> 

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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