[gmx-users] pdb2gmx -water-> grompp; grompp error
Justin A. Lemkul
jalemkul at vt.edu
Tue Aug 25 20:38:09 CEST 2009
Paymon Pirzadeh wrote:
> OK! That's fine. But what if I do not have permissions to make such
> changes in the itp files? Also, isn't that the case that when you define
That's why I said copy the force field files into your local directory. Once
there, you can modify them.
> sth for the second time, grompp will take the second one? Sorry for mass
> of e-mail!
>
That is only true in the case of .mdp files.
-Justin
> Payman
>
>
>
> On Tue, 2009-08-25 at 14:26 -0400, Justin A. Lemkul wrote:
>> 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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>>
>
>
--
========================================
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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