[gmx-users] pdb2gmx -water-> grompp; grompp error
Paymon Pirzadeh
ppirzade at ucalgary.ca
Tue Aug 25 21:26:57 CEST 2009
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?
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
> >>
> >> ========================================
> >> _______________________________________________
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> >
> >
>
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