[gmx-users] pdb2gmx -water-> grompp; grompp error

[Justin A. Lemkul]

Paymon Pirzadeh wrote:
> Hello,
> Just a reminder that I had troubled with combination rules between my
> water model and GROMACS forcefields. I fixed the problem by adjusting my
> water model's parameters. BUT, now, I specified the new parameters in
> my .itp file under [ atomtype ] category and grompp makes errors out of
> the orders. Now I am using OPLSaa. I suspect again the problem comes
> from the presence of the second [atomtype ]. How can I keep my new
> parameters and use them in my water model's itp file? Or should I change
> these parameters in the OPLSaa.itp file? 

You can't have a second [atomtypes] directive.  You can add new parameters to 
ffoplsaanb.itp to account for the atom types you are implementing, though.

If you want anything more specific, you'll probably have to provide the topology 
file you're working with, as well as any actual error messages you're seeing.

-Justin

> Regards,
> 
> Payman  
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> On Wed, 2009-08-19 at 10:20 +1000, Mark Abraham wrote:
>> 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)?
>> A water model that isn't compatible with the model of the solutes isn't 
>> of any value, so it looks like you have put the cart before the horse.
>>
>> Mark
>>
>>> 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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