[gmx-users] pdb2gmx -water-> grompp

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 19 00:52:04 CEST 2009

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.


> 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


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