[gmx-users] pdb2gmx -water-> grompp; grompp error
Justin A. Lemkul
jalemkul at vt.edu
Tue Aug 25 20:26:57 CEST 2009
Paymon Pirzadeh wrote:
> I have done that already! I use my local copy to make my files. but how
> can I get rid of this error? get into the oplsaanb.itp or include this
> water model in the topology file before oplsaa.itp?
>
I don't understand what you're saying you've already done.
The problem is this: when grompp attempts to assemble the .tpr file, it reads
all of the information from the ffoplsaa*.itp files. It finds the directives
like [defaults], [atomtypes], etc in a pre-defined order. If, later, it finds a
duplicate of these directives, it complains. So when you #include your .itp
file with new [atomtypes], it generates the error because it is a duplicate
directive. You have to include the new atom types in ffoplsaanb.itp in the
[atomtypes] directive of this file. The rest of the topology shouldn't cause a
problem, just the [atomtypes] directive.
-Justin
> Payman
>
>
>
>
>
> On Tue, 2009-08-25 at 14:14 -0400, Justin A. Lemkul wrote:
>> Paymon Pirzadeh wrote:
>>> OK!
>>> here is the .itp file which I generated. I might upload it because it
>>> has passed the initial tests.
>>>
>>> ; This is an itp file to describe water's six-site model by H. Nada and
>>> J.P. J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413
>>> (2003)
>>> ; This model is a combination of TIP4P and TIP5P. It has three LJ sites
>>> and 3 Coulomb sites
>>> ; O-H bond length is 0.980A, HOH angle is 108.00degrees, LOL angle is
>>> 111.00 degrees, O-M and O-L are about 0.230A and 0.8892A respectively
>>>
>>> [ defaults ]
>>> ; non-bondedtype combrule genpairs FudgeLJ
>>> FudgeQQ N
>>> 1 2 NO
>>>
>>> [ atomtypes ]
>>> ;name mass charge ptype c6 c12
>>> OW 15.9994 0.0 A 0.3115 0.714845562
>>> HW 1.00800 0.477 A 0.0673 0.11541
>>> MW 0.000 -0.866 D 0.00 0.00
>>> LW 0.00 -0.044 D 0.00 0.00
>>>
>>> [ moleculetype ]
>>> ;molname nrexcl
>>> SOL 2
>>>
>>> [ atoms ]
>>> ; nr atomtype resnr residuename atom cgnr charge
>>> 1 OW 1 SOL OW 1 0.0
>>> 2 HW 1 SOL HW1 1 0.477
>>> 3 HW 1 SOL HW2 1 0.477
>>> 4 MW 1 SOL MW 1 -0.866
>>> 5 LW 1 SOL LP1 1 -0.044
>>> 6 LW 1 SOL LP2 1 -0.044
>>>
>>> [ settles ]
>>> ; OW function doh dhh
>>> 1 1 0.0980 0.15856
>>>
>>> [ dummies3 ]
>>> ; These set of parameters are for M site which can be easily calculated
>>> using TIP4P calculations from tip4p.itp
>>> ; So, it will be described as dummy site 3: r(v)= r(i) + a*(r(i)-r(j)) +
>>> b*(r(i)-r(k))
>>> ; const = |OH|/{|OH|*cos(HOH/2)} => Due to vector algebra a=b=const/2.
>>> Remember that OM is in the same direction of OH bonds.
>>> ; Remember this site is in the same plane of OH bonds; so, its function
>>> 1
>>> ;
>>> ; site from function a b
>>> 4 1 2 3 1 0.199642536 0.199642536
>>>
>>> ; Now we define the position of L sites which can be obtained from
>>> tip5p.itp
>>> ; So, it will be described as dummy site 3out: r(v) = r(i) +
>>> a*(r(i)-r(j)) + b*(r(i)-r(k)) + c*(r(ij)Xr(ik))
>>> ; const1 = {|OL|*cos(LOL/2)}/{|OH|*cos(HOH/2)} => Due to vector algebra
>>> |a|=|b|=const/2. since the lone pairs are in opposite direction of OH
>>> bonds, a minus sign is added. This part is similar to M site.
>>> ; const2 = {|OL|*sin(LOL/2)}/{|OH|*|OH|*sin(HOH)} => The denominator is
>>> the magnitude of vector product of OH bonds.
>>> ; This sites are tetrahedral sites; so, its function 4
>>> ;
>>> ; site from function a b
>>> c
>>> 5 1 2 3 4 -0.437172388 -0.437172388
>>> 8.022961206
>>> 6 1 2 3 4 -0.437172388 -0.437172388
>>> -8.022961206
>>>
>>> [ exclusions ]
>>> 1 2 3 4 5 6
>>> 2 1 3 4 5 6
>>> 3 1 2 4 5 6
>>> 4 1 2 3 5 6
>>> 5 1 2 3 4 6
>>> 6 1 2 3 4 5
>>>
>>> and here is the message I get from grompp:
>>>
>>> Program grompp_d_mpi, VERSION 4.0.5
>>> Source code file: topio.c, line: 415
>>>
>>> Fatal error:
>>> Syntax error - File sixsitewater.itp, line 12
>>> Last line read:
>>> '[ atomtypes ]'
>>> Invalid order for directive atomtypes
>>> -------------------------------------------------------
>>>
>>> I believe the original files of GROMACS need admin permissions which I
>>> do not have on the cluster that I am currently using and I am not sure
>>> if that might not cause troubles for other users. So, I thought how I
>>> can keep the changes local.
>>>
>> Make a copy in your local directory; grompp will use these before looking for
>> system-wide files. As a general rule, whenever developing new parameters or
>> adjusting files, do so locally before potentially messing yourself (or others) up :)
>>
>> -Justin
>>
>>> Payman
>>>
>>>
>>> On Tue, 2009-08-25 at 13:53 -0400, Justin A. Lemkul wrote:
>>>> 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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