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

Justin A. Lemkul jalemkul at vt.edu
Tue Aug 25 21:59:57 CEST 2009



Paymon Pirzadeh wrote:
> When I look at the .top file generated by pdb2gmx, the last lines show
> how this -0.99 is generated:
> 
>    442   opls_302     37    ARG     CZ    138       0.64     12.011   ;
> qtot -0.33
>    443   opls_300     37    ARG    NH1    139       -0.8    14.0067   ;
> qtot -1.13
>    444   opls_301     37    ARG   HH11    139       0.46      1.008   ;
> qtot -0.67
>    445   opls_301     37    ARG   HH12    139       0.46      1.008   ;
> qtot -0.21
>    446   opls_300     37    ARG    NH2    140       -0.8    14.0067   ;
> qtot -1.01
>    447   opls_301     37    ARG   HH21    140       0.46      1.008   ;
> qtot -0.55
>    448   opls_301     37    ARG   HH22    140       0.46      1.008   ;
> qtot -0.09
>    449   opls_271     37    ARG      C    141        0.7     12.011   ;
> qtot 0.61
>    450   opls_272     37    ARG     O1    141       -0.8    15.9994   ;
> qtot -0.19
>    451   opls_272     37    ARG     O2    141       -0.8    15.9994   ;
> qtot -0.99
> 
> The charged side-chains are Arg, Lys, 2 * Asp and Glu. Since the pH of
> simulation is supposed to be close to 7.0, I believe one of the
> negatively-charged side chains needs to be neutralized. That's why I
> think one Na+ might be helpful.
> 

That's probably correct.  I just wanted to verify what was in your system.  If 
you just had water, it made no sense.  But with a protein involved with lots of 
partial charges, these rounding issues do occur.  You really do have a system 
with -1 charge.

-Justin

> Payman
> 
> 
> On Tue, 2009-08-25 at 15:45 -0400, Justin A. Lemkul wrote:
>> Paymon Pirzadeh wrote:
>>> OK! It worked! Thanks a lot again. But I have a final technical
>>> question. After running grompp, it shows that my box has a net charge of
>>> -0.99 . Do you think adding one Na+ and reducing the charge to +0.01 is
>>> OK?! or even this 0.01 charge will cause me troubles?
>> Depending on the size of your system, rounding errors can occur.  It is unusual 
>> that the hundredths place would be showing this error.  Usually you'd get 
>> something like 0.99998 or something.  Your water topology has a zero net charge; 
>> is there something else in your system causing the -1 charge?
>>
>> Adding a single Na+ to neutralize the charge may be appropriate, but that's up 
>> to you based on what's in your system (something else may be broken, but I just 
>> don't know).
>>
>> -Justin
>>
>>> Sorry for tons of e-mails.
>>> regards,
>>>
>>> Payman
>>>
>>>
>>> On Tue, 2009-08-25 at 14:38 -0400, Justin A. Lemkul wrote:
>>>> 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
>>>>>>
>>>>>> ========================================
>>>>>> _______________________________________________
>>>>>> gmx-users mailing list    gmx-users at gromacs.org
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>>>>>> Please search the archive at http://www.gromacs.org/search before posting!
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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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