[gmx-users] pdb2gmx -water-> grompp; grompp error
Paymon Pirzadeh
ppirzade at ucalgary.ca
Tue Aug 25 20:23:05 CEST 2009
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?
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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