[gmx-users] pdb2gmx -water-> grompp; grompp error
Justin A. Lemkul
jalemkul at vt.edu
Tue Aug 25 20:14:50 CEST 2009
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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